Merge pull request #471 from nfdi4plants/ceplas-arcify-workshop

Ceplas arcify workshop

src/docs/_sidebars/mainSidebar.md

@@ -163,7 +163,6 @@
 ### [CEPLAS ARC Trainings – Spring 2024](/docs/teaching-materials/events-2024/2024-04-03_CEPLAS-ARC-Trainings/index.html)
 ### [MibiNet CEPLAS DataPLANT Tool-Workshops](/docs/teaching-materials/events-2024/2024-04-11_MibiNet-CEPLAS-ARC-Trainings/index.html)
 ### [TRR175 Tutzing Retreat](/docs/teaching-materials/events-2024/2024-06-19-TRR175-Tutzing-Retreat/index.html)
-
-
+### [CEPLAS ARCify your research project](/docs/teaching-materials/events-2024/2024-10-24_CEPLAS-ARCify-your-research-project/index.html)
 
 # [Frequently Asked Questions](/docs/faqs/faqs.html)

src/docs/teaching-materials/events-2024/2024-10-24_CEPLAS-ARCify-your-research-project/00-Welcome.md

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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
+---
+
+#  ARCify your research project
+
+<!--  _color: white; -->
+<!-- _paginate: false -->
+<style scoped>section {background: none; background-color: white;}</style>
+
+October, 2024
+
+Dominik Brilhaus (CEPLAS)
+Sabrina Zander (MibiNet)
+
+![bg fit](./../../../img/background_title_ceplas.drawio.svg)
+
+---
+
+# Goals
+
+- First few steps into ARC ecosystem
+- Move existing datasets into ARCs
+- Share them via the DataHUB
+- Annotate with metadata
+
+![bg right w:500](./../../../img/ceplas-ARCs.drawio.svg)
+
+---
+
+# House-keeping
+
+<div class="two-columns">
+  <div>
+
+  - Use the pad to raise questions and feedback
+  - Copy / paste links (hands-on)
+
+  </div>
+
+  <div>
+  <a href="https://pad.hhu.de/8bwBC7pyRL2tFFOWMQzm1Q?edit" target="_blank"> <img src="./qr-code-pad.png"></a>
+  </div>
+</div>
+
+---
+
+# Training Materials
+
+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/)
+
+---
+
+# Resources &ndash; join the open source movement
+
+### <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)
+
+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>
+
+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>
+
+:bulb: You can help us by raising issues, bugs, ideas...
+
+:rocket: NEW! ARC website: <a href="https://arc-rdm.org" target="_blank">https://arc-rdm.org</a>
+
+---
+
+# Continuous support
+
+Data managers in Düsseldorf, Cologne, Jülich and close by (CEPLAS, MibiNet, TRR341) offer support.
+
+1. Slack Workspace for ad hoc support
+2. Monthly user meeting (2nd Friday of the month)
+
+[&rarr; Details](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/teaching-materials/disseminations/ARC-user-support_HHU-Uoc-FZJ/arc-user-support.html).
+
+<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>

src/docs/teaching-materials/events-2024/2024-10-24_CEPLAS-ARCify-your-research-project/04-CEPLAS-CurrentState.md

@@ -0,0 +1,34 @@
+---
+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
+---
+
+# CEPLAS – One cluster, four locations
+
+![w:800](./../../../img/data-fragmentation-ceplas00.drawio.png)
+
+---
+
+# Data silos impede collaboration
+
+![w:800](./../../../img/data-fragmentation-ceplas01.drawio.png)
+
+---
+
+# Data silos impede collaboration
+
+![w:800](./../../../img/data-fragmentation-ceplas02.drawio.png)
+
+---
+
+# Missing interfaces impede collaboration
+
+![w:800](./../../../img/HHU-services-withoutDataHUB.drawio.png)

src/docs/teaching-materials/events-2024/2024-10-24_CEPLAS-ARCify-your-research-project/10-Overview-DataPLANT.md

@@ -0,0 +1,189 @@
+---
+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
+---
+
+
+# Data Stewardship between DataPLANT and the community <!-- fit -->
+
+![w:880](./../../../img/DataPLANT-collaborationCEPLAS.drawio.png)
+
+---
+
+# Annotated Research Context (ARC)
+
+![width:800](./start-here/arc-bag.svg)
+
+Your entire investigation in a single unified bag
+
+---
+
+# You can store your ARC in the DataHUB
+
+![w:800](./../../../img/DataPLANT_BigPicture_seq2.png)
+
+---
+
+# ARCs are versioned
+
+![w:800](./../../../img/DataPLANT_BigPicture_seq3.png)
+
+---
+
+# You can invite collaborators
+
+![w:800](./../../../img/DataPLANT_BigPicture_seq4.png)
+
+---
+
+# Collaborate and contribute
+
+![w:800](./../../../img/DataPLANT_BigPicture_seq5.png)
+
+---
+
+# Reuse data in ARCs
+
+![w:800](./../../../img/DataPLANT_BigPicture_seq6.png)
+
+---
+
+# Publish your ARC
+
+![w:800](./../../../img/DataPLANT_BigPicture_seq7.png)
+
+---
+
+
+# Publish your ARC, get a DOI
+
+![w:800px](https://www.nfdi4plants.org/nfdi4plants.knowledgebase/docs/img/ARC_SeamlessPublication.svg)
+
+---
+
+# ARC as single-entry point
+
+![w:900](./../../../img/ARC-publication-outlets.drawio.png)
+
+---
+
+# Data analysis and workflows
+
+![w:800](./../../../img/tpj16474-fig-0005-m.jpg)
+
+<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>
+
+---
+
+# Galaxy integration: Extra value for plant research
+
+<div class="two-columns">
+<div>
+
+![](./../../../img/galaxy-integration.drawio.png)
+
+</div>
+
+<div>
+
+- Full ARC compatibility
+- Automated metadata generation
+- Specialized tools and workflows for ‘omics processing and analysis
+- Public repository compatibility
+- Galaxy teaching resource for data analysis
+
+</div>
+</div>
+
+
+---
+
+# Enabling platforms
+
+
+<div class="two-columns">
+  <div>
+
+  - Streamlined exchange of (meta)data
+  - Communication and project management
+
+  </div><div>
+
+  ![](./../../../img/ceplas-enablingPlatforms.drawio.png)
+
+  </div>
+</div>
+
+
+---
+
+# Streamlined data exchange
+
+<img src="./../../../img/enablingPlatform-FileShare.drawio.png" style="width:60%;display: block;margin-left: auto;margin-right: auto;">
+
+---
+
+# Meet your collaborators in an ARC
+
+<img src="./../../../img/enablingPlatform-Timeline.drawio.png" style="width:80%;display: block;margin-left: auto;margin-right: auto;">
+
+---
+
+# The ARC ecosystem
+
+![w:850](./../../../img/ARC-ecosystem-10.drawio.png)
+
+---
+
+# What does an ARC look like?
+
+![width:950](./../../../img/ARC_fillWithData_seq1.png)
+
+---
+
+# ARCs store experimental data
+
+![width:950](./../../../img/ARC_fillWithData_seq3.png)
+
+---
+
+# Computations can be run inside ARCs
+
+![width:950](./../../../img/ARC_fillWithData_seq5.png)
+
+---
+
+# ARCs come with comprehensive metadata
+
+![width:950](./../../../img/ARC_fillWithData_seq6.png)
+
+---
+
+# ARC builds on standards
+
+<div class="two-columns">
+  <div>
+
+  ![w:500](./../../../img/ARC_BuildsOnStandards3.png)
+
+  </div>
+  <div>
+
+  - RO-Crate: standardized exchange
+  - ISA: structured, machine-readable metadata
+  - CWL: reproducible, re-usable data analysis
+  - Git: version control
+
+  </div>
+</div>
+
+<span class="footer-reference">https://isa-tools.org/ | https://www.commonwl.org/
+https://www.researchobject.org/ro-crate/ | https://git-scm.com</span>