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Ceplas arcify workshop
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--- | ||
marp: true | ||
theme: marp-theme_dataplant-ceplas-ccby | ||
paginate: true | ||
license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)' | ||
title: Welcome and Intro | ||
author: | ||
- name: Dominik Brilhaus | ||
github: https://github.com/brilator | ||
orcid: https://orcid.org/0000-0001-9021-3197 | ||
--- | ||
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# ARCify your research project | ||
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<!-- _color: white; --> | ||
<!-- _paginate: false --> | ||
<style scoped>section {background: none; background-color: white;}</style> | ||
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October, 2024 | ||
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Dominik Brilhaus (CEPLAS) | ||
Sabrina Zander (MibiNet) | ||
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![bg fit](./../../../img/background_title_ceplas.drawio.svg) | ||
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--- | ||
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# Goals | ||
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- First few steps into ARC ecosystem | ||
- Move existing datasets into ARCs | ||
- Share them via the DataHUB | ||
- Annotate with metadata | ||
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![bg right w:500](./../../../img/ceplas-ARCs.drawio.svg) | ||
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--- | ||
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# House-keeping | ||
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<div class="two-columns"> | ||
<div> | ||
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- Use the pad to raise questions and feedback | ||
- Copy / paste links (hands-on) | ||
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</div> | ||
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<div> | ||
<a href="https://pad.hhu.de/8bwBC7pyRL2tFFOWMQzm1Q?edit" target="_blank"> <img src="./qr-code-pad.png"></a> | ||
</div> | ||
</div> | ||
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--- | ||
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# Training Materials | ||
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Slides are shared via [DataPLANT knowledge base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/teaching-materials/events-2024/2024-10-24_CEPLAS-ARCify-your-research-project/) | ||
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--- | ||
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# Resources – join the open source movement | ||
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### <img align="left" style="height:35px" src='https://raw.githubusercontent.com/nfdi4plants/Branding/7e7d442aafeaa767b9c14a63a16e459dadcbdaaf/logos/DataPLANT/DataPLANT_logo_minimal_rounded_bg_darkblue.svg'/> DataPLANT (nfdi4plants) | ||
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DataPLANT Website: <a href="https://nfdi4plants.org/" target="_blank">https://nfdi4plants.org/</a> | ||
Knowledge Base: <a href="https://nfdi4plants.org/nfdi4plants.knowledgebase/" target="_blank">https://nfdi4plants.org/nfdi4plants.knowledgebase/</a> | ||
DataHUB: <a href="https://git.nfdi4plants.org" target="_blank">https://git.nfdi4plants.org</a> | ||
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GitHub: <a href="https://github.com/nfdi4plants" target="_blank">https://github.com/nfdi4plants</a> | ||
HelpDesk: <a href="https://helpdesk.nfdi4plants.org" target="_blank">https://helpdesk.nfdi4plants.org</a> | ||
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:bulb: You can help us by raising issues, bugs, ideas... | ||
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:rocket: NEW! ARC website: <a href="https://arc-rdm.org" target="_blank">https://arc-rdm.org</a> | ||
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--- | ||
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# Continuous support | ||
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Data managers in Düsseldorf, Cologne, Jülich and close by (CEPLAS, MibiNet, TRR341) offer support. | ||
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1. Slack Workspace for ad hoc support | ||
2. Monthly user meeting (2nd Friday of the month) | ||
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[→ Details](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/teaching-materials/disseminations/ARC-user-support_HHU-Uoc-FZJ/arc-user-support.html). | ||
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<div> | ||
<img style="height:40px;margin-right:50px" src='https://www.ceplas.eu/typo3conf/ext/fksitepackage/Resources/Public/Images/CEPLAS-Logo.svg'/> | ||
<img style="height:100px;margin-right:50px" src='https://trr341.uni-koeln.de/sites/crc_trr_341/TRR341_logo.png'/> | ||
<img style="height:70px;margin-right:50px" src='https://www.sfb1535.hhu.de/fileadmin/redaktion/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Biologie/SFB1535/Bilder/MibiNet.png'/> | ||
</div> |
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--- | ||
marp: true | ||
paginate: true | ||
theme: marp-theme_dataplant-ceplas-ccby | ||
license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)' | ||
date: 2024-03-25 | ||
title: CEPLAS current state | ||
author: | ||
- name: Dominik Brilhaus | ||
github: https://github.com/brilator | ||
orcid: https://orcid.org/0000-0001-9021-3197 | ||
--- | ||
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# CEPLAS – One cluster, four locations | ||
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![w:800](./../../../img/data-fragmentation-ceplas00.drawio.png) | ||
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--- | ||
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# Data silos impede collaboration | ||
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![w:800](./../../../img/data-fragmentation-ceplas01.drawio.png) | ||
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--- | ||
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# Data silos impede collaboration | ||
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![w:800](./../../../img/data-fragmentation-ceplas02.drawio.png) | ||
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--- | ||
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# Missing interfaces impede collaboration | ||
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![w:800](./../../../img/HHU-services-withoutDataHUB.drawio.png) |
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--- | ||
marp: true | ||
paginate: true | ||
theme: marp-theme_dataplant-ceplas-ccby | ||
license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)' | ||
title: Overview DataPLANT | ||
date: 2023-11-14 | ||
author: | ||
- name: Dominik Brilhaus | ||
github: https://github.com/brilator | ||
orcid: https://orcid.org/0000-0001-9021-3197 | ||
--- | ||
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# Data Stewardship between DataPLANT and the community <!-- fit --> | ||
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![w:880](./../../../img/DataPLANT-collaborationCEPLAS.drawio.png) | ||
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--- | ||
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# Annotated Research Context (ARC) | ||
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![width:800](./start-here/arc-bag.svg) | ||
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Your entire investigation in a single unified bag | ||
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--- | ||
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# You can store your ARC in the DataHUB | ||
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![w:800](./../../../img/DataPLANT_BigPicture_seq2.png) | ||
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--- | ||
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# ARCs are versioned | ||
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![w:800](./../../../img/DataPLANT_BigPicture_seq3.png) | ||
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--- | ||
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# You can invite collaborators | ||
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![w:800](./../../../img/DataPLANT_BigPicture_seq4.png) | ||
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--- | ||
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# Collaborate and contribute | ||
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![w:800](./../../../img/DataPLANT_BigPicture_seq5.png) | ||
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--- | ||
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# Reuse data in ARCs | ||
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![w:800](./../../../img/DataPLANT_BigPicture_seq6.png) | ||
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--- | ||
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# Publish your ARC | ||
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![w:800](./../../../img/DataPLANT_BigPicture_seq7.png) | ||
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--- | ||
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# Publish your ARC, get a DOI | ||
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![w:800px](https://www.nfdi4plants.org/nfdi4plants.knowledgebase/docs/img/ARC_SeamlessPublication.svg) | ||
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--- | ||
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# ARC as single-entry point | ||
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![w:900](./../../../img/ARC-publication-outlets.drawio.png) | ||
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--- | ||
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# Data analysis and workflows | ||
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![w:800](./../../../img/tpj16474-fig-0005-m.jpg) | ||
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<span class="footer-reference"> Weil, H.L., Schneider, K., et al. (2023), PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research. Plant J. https://doi.org/10.1111/tpj.16474 </span> | ||
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--- | ||
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# Galaxy integration: Extra value for plant research | ||
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<div class="two-columns"> | ||
<div> | ||
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![](./../../../img/galaxy-integration.drawio.png) | ||
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</div> | ||
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<div> | ||
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- Full ARC compatibility | ||
- Automated metadata generation | ||
- Specialized tools and workflows for ‘omics processing and analysis | ||
- Public repository compatibility | ||
- Galaxy teaching resource for data analysis | ||
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</div> | ||
</div> | ||
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--- | ||
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# Enabling platforms | ||
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<div class="two-columns"> | ||
<div> | ||
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- Streamlined exchange of (meta)data | ||
- Communication and project management | ||
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</div><div> | ||
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![](./../../../img/ceplas-enablingPlatforms.drawio.png) | ||
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</div> | ||
</div> | ||
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--- | ||
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# Streamlined data exchange | ||
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<img src="./../../../img/enablingPlatform-FileShare.drawio.png" style="width:60%;display: block;margin-left: auto;margin-right: auto;"> | ||
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--- | ||
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# Meet your collaborators in an ARC | ||
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<img src="./../../../img/enablingPlatform-Timeline.drawio.png" style="width:80%;display: block;margin-left: auto;margin-right: auto;"> | ||
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--- | ||
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# The ARC ecosystem | ||
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![w:850](./../../../img/ARC-ecosystem-10.drawio.png) | ||
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--- | ||
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# What does an ARC look like? | ||
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![width:950](./../../../img/ARC_fillWithData_seq1.png) | ||
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--- | ||
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# ARCs store experimental data | ||
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![width:950](./../../../img/ARC_fillWithData_seq3.png) | ||
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--- | ||
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# Computations can be run inside ARCs | ||
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![width:950](./../../../img/ARC_fillWithData_seq5.png) | ||
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--- | ||
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# ARCs come with comprehensive metadata | ||
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![width:950](./../../../img/ARC_fillWithData_seq6.png) | ||
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--- | ||
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# ARC builds on standards | ||
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<div class="two-columns"> | ||
<div> | ||
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![w:500](./../../../img/ARC_BuildsOnStandards3.png) | ||
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</div> | ||
<div> | ||
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- RO-Crate: standardized exchange | ||
- ISA: structured, machine-readable metadata | ||
- CWL: reproducible, re-usable data analysis | ||
- Git: version control | ||
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</div> | ||
</div> | ||
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<span class="footer-reference">https://isa-tools.org/ | https://www.commonwl.org/ | ||
https://www.researchobject.org/ro-crate/ | https://git-scm.com</span> |
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