MArch 2024 workshop: links to training materials

[haesleinhuepf]

We should go through these links and check if we have them in our database and otherwise poentially add them:

https://www.ugent.be/en/research/openscience/datamanagement https://www.go-fair.org/resources/rdm-starter-kit/ forschungsdaten.info
https://f1000research.com/slides/11-746
https://www.mdpi.com/2304-6775/5/1/2 https://www.nature.com/articles/sdata201618
https://www.go-fair.org/fair-principles/ https://www.nature.com/articles/sdata201618 https://www.nature.com/articles/s41431-018-0160-0
https://pubmed.ncbi.nlm.nih.gov/36371407/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9271325/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015/
Griffin, P., et al., Best practice data life cycle approaches for the life sciences [version 2; peer review: 2 approved]. F1000Research, 2018. 6(1618). DOI: https://doi.org/10.12688/f1000research.12344.2 https://doi.org/10.11588/heidok.00029489 https://rdmkit.elixir-europe.org/data_life_cycle https://tess.elixir-europe.org/search?q=data+life+cycle#materials https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/ https://bausteine-fdm.de/article/view/7945 https://www.o-bib.de/bib/article/view/2018H2S1-13 https://discovery.ucl.ac.uk/id/eprint/1546596/1/26_Learn_Guidance_137-140.pdf
https://dsw.fairdata.solutions/ https://base4nfdi.de/images/AbstractDMP4NFDI.pdf https://ds-wizard.org/ https://rdmorganiser.github.io/ https://focalplane.biologists.com/2023/11/06/creating-a-research-data-management-plan-using-chatgpt/

Sharing & Licensing, https://f1000research.com/slides/10-519 https://hup.sub.uni-hamburg.de/oa-pub/catalog/book/205

The Carpentries
Schmidt, C., Bortolomeazzi, M., Boissonnet, T., Fortmann-Grote, C., Dohle, J., Zentis, P., Kandpal, N., Kunis, S., Zobel, T., Weidtkamp-Peters, S., & Ferrando-May, E. (2023). I3D:bio's OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training. Zenodo. https://doi.org/10.5281/zenodo.8323588 https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html Fiji plugin "simple-omero-client" Fiji plugin "omero_batch-plugin"
https://omero-guides.readthedocs.io/en/latest/python/docs/gettingstarted.html https://docs.openmicroscopy.org/omero/5.6.0/developers/Python.html https://github.com/ome/omero-guide-python
https://wiki-biop.epfl.ch/en/data-management/omero/qupath https://omero-guides.readthedocs.io/en/latest/qupath/docs/index.html

https://usegalaxy-eu.github.io/posts/2020/11/23/OMERO-post/ https://training.galaxyproject.org/
BIOMERO

https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/
( https://guide-kvpairs-scripts.readthedocs.io/en/latest/ -> will be moved to omero-guides) Excel sheet with Macros for dropdown and export as .csv Annotations using Tabbles and OMERO.script Fiji plugin "simple-omero-client" Fiji plugin "omero_batch-plugin"

REMBI , https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47 NBO QUAREP-LiMi https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/ https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.871228/full https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/ https://www.nature.com/articles/s41597-023-02367-w

GitHub - cmohl2013/omero-arc: Library to export OMERO projects to ARC repositories https://www.fdm.tu-clausthal.de/fileadmin/FDM/documents/Manual_eLab_v0.3_20200323.pdf

https://focalplane.biologists.com/2021/09/04/collaborative-bio-image-analysis-script-editing-with-git/

http://opendatahandbook.org/guide/en/what-is-open-data/ https://www.fosteropenscience.eu/learning/use-open-data-in-teaching/#/id/5b06ca3ba8216e322da360b6
https://web.library.uq.edu.au/blog/2022/03/five-great-reasons-share-your-research-data https://www.publisso.de/en/advice/publishing-advice-faqs/research-data
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/image-data-repositories/ 10.12688/f1000research.121714.2
https://gerbi-gmb.de/2023/06/01/finding-and-choosing-a-repository/ https://www.re3data.org/
https://www.go-fair.org/fair-principles/

Cultlivating Open Training (Slides) https://zenodo.org/records/10654775 https://focalplane.biologists.com/2023/05/06/if-you-license-it-itll-be-harder-to-steal-it-why-we-should-license-our-work/
https://www.ebi.ac.uk/bioimage-archive/submit/ https://www.sciencedirect.com/science/article/pii/S0022283622000791?via%3Dihub
https://www.nature.com/articles/nmeth.4326
https://focalplane.biologists.com/2023/02/15/sharing-research-data-with-zenodo/ https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/

nfdi.de forschungsdaten.info

Cultlivating Open Training (Slides) https://zenodo.org/records/10654775 https://doi.org/10.1371/journal.pcbi.1007854

Data Stewardship goes Germany https://www.nature.com/articles/s41431-018-0160-0

https://omero-fbi.fr/slides/elmi23_cfd/main.html#/title-slide
Youtube channel OME Youtube channel Glencoe Youtube videos Eric Ratamero I3D:bio training material collection
https://www.orca.nrw/searchresults?searchbox=%22elabftw%22&orca_show_all_of=result_media
https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html
OMERO-cli-transfer tool

NGFF spec/schema NGFF validator
https://www.glencoesoftware.com/products/ngff-converter/ https://github.com/glencoesoftware/bioformats2raw https://github.com/glencoesoftware/raw2ometiff BioFormats CLI toolkit

https://www.nature.com/collections/djiciihhjh https://forum.image.sc/t/checklists-for-publishing-images-and-image-analysis/86304
https://workflowhub.eu/ https://galaxyproject.org/learn/advanced-workflow/ https://galaxy-au-training.github.io/tutorials/modules/workflows/
https://training.galaxyproject.org/ https://www.knime.com/community/image-processing
https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/

[lea-33]

@haesleinhuepf could you maybe assign me to that issue? I'm already working on it but can't assign myself (yet).