add ARC Club slides

nfdi4plants · Nov 14, 2023 · b3804da · b3804da
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diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.html b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.html
diff --git a/...eaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.md b/...eaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.md
@@ -17,6 +17,7 @@ author:
 <style scoped>section {background: none; background-color: white;}</style>
 
 <br>
+
 November 15<sup>th</sup>, 2023
 Dominik Brilhaus, CEPLAS Data Science
 
@@ -115,7 +116,23 @@ Slides will be shared via DataPLANT knowledge base
 
 ---
 
-# Let's draw a typical lab workflow from your lab :pencil:
+# Let's draw a typical lab workflow from your lab :pencil: <!-- fit -->
+
+---
+
+# Resources
+
+### <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)
+
+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...
 
 ---
 

diff --git a/.../teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.html b/.../teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.html
diff --git a/...g-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.md b/...g-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.md
@@ -0,0 +1,284 @@
+---
+marp: true
+paginate: true
+theme: marp-theme_dataplant-ceplas-ccby
+license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)'
+title: ARC Ecosystem Demo
+date: 2023-11-14
+author:
+- name: Dominik Brilhaus
+  github: https://github.com/brilator
+  orcid: https://orcid.org/0000-0001-9021-3197
+---
+
+<style>
+
+figcaption {
+  font-size: 10px;
+  font-style: italic;
+}
+
+.reference-bgright {
+  font-size:15px;
+  line-height: 1.2em;
+  position: fixed;
+  right: 0px;
+  bottom: 0px;
+  transform: translate(-50%, -50%);
+  margin: 0 auto;
+}
+
+</style>
+
+# The ARC ecosystem
+
+<!--  _color: white; -->
+<!-- _paginate: false -->
+
+<style scoped>section {background: none; background-color: white;}</style>
+
+### *A FAIR RDM journey along a (mutable) data life cycle*
+
+<br>
+
+![bg fit](./../../../img/background_title_ceplas.drawio.svg)
+
+---
+
+# Data Stewardship between DataPLANT and the community  <!-- fit -->
+
+![w:880](././../../../img/DataPLANT-collaborationCEPLAS.drawio.png)
+
+---
+
+# The research data life cycle
+
+<br>
+
+![w:350](./../../../img/RDMkit-data_life_cycle_9.svg)
+
+<span class="footer-reference">https://rdmkit.elixir-europe.org, [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)</span>
+
+---
+
+# Annotated Research Context (ARC)
+
+![width:950](./../../../img/ARC_DataCentricIntegration_img1.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
+
+![w:880](./../../../img/ARC_BuildsOnStandards2.png)
+
+<span class="footer-reference">https://isa-tools.org/ | https://www.commonwl.org/
+https://www.researchobject.org/ro-crate/ | https://git-scm.com</span>
+
+---
+
+<!-- _paginate: false -->
+
+<style scoped>section {background: none; background-color: white;}</style>
+
+---
+
+
+# Collect <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-02-collect.png'/>
+
+![width:800](./../../../img/ARC_fillWithData_experimental.png)
+
+<!-- 
+
+- create study folder
+  - take a picture (add more demo pictures)
+- create assay folder
+  - add fastq data
+
+-->
+
+---
+
+# Process (e.g. annotate)  <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-03-process.png'/>
+
+<style scoped>
+
+section p img {
+width: 900px;
+height: 400px;
+object-fit: cover;
+object-position: 50% 60%;
+/* display: block; */;
+}
+</style>
+
+![](./../../../img/Swate_metadataTemplates.png)
+
+<!-- 
+
+- annotate plant samples
+- annotate rnaseq extraction -->
+
+---
+
+# Analyse <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-04-analyse.png'/>
+
+<!-- 
+- run fastqc
+- receive back results
+-->
+
+![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>
+
+---
+
+# Preserve  <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-05-preserve.png'/>
+
+<!--
+1. Validation: CQC on each DataHUB commit
+2. Publication: DOI
+-->
+
+![h:400](./../../../img/tpj16474-fig-0008-m-modified.png)
+
+<span class="footer-reference"> adapted from 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>
+
+---
+
+# Preserve and publish <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-05-preserve.png'/>
+
+<!--
+1. Validation: CQC on each DataHUB commit
+2. Publication: DOI
+-->
+
+![h:400](././../../../img/tpj16474-fig-0008-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>
+
+---
+
+# Share and collaborate <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-06-share.png'/>
+
+![w:700](./../../../img/ARC_DataSharing_Experts02_img1.png)
+
+---
+
+# Reuse <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-07-reuse.png'/>
+
+![w:800](./../../../img/tpj16474-fig-0001-m.jpg)
+
+<!-- 
+- via ARC https://arcregistry.nfdi4plants.org/arcsearch
+- via ISA https://arcregistry.nfdi4plants.org/isasearch 
+-->
+
+<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>
+
+---
+
+# **Mutable** data life cycle
+
+![w:700](./../../../img/tpj16474-fig-0006-m.jpg)
+
+<!-- 
+
+- Invite other (demo) account
+- add notes from there
+-->
+
+<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>
+
+---
+
+# Plan &ndash; ARC scale <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-01-plan.png'/>
+
+![w:800](./../../../img/tpj16474-fig-0007-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>
+
+<!--
+ 
+ - **ARCitect**: Create empty ARC
+   - description
+   - author
+     - first name
+     - last name
+     - email
+ - **ARCitect**: Upload ARC to DataHUB
+ - **DataHUB**
+   - Discuss, collect meeting minutes in Wiki
+   - design / plant investigation (datahub wiki, issues)
+
+-->
+
+---
+
+# Plan  &ndash; proposal scale <img align="left" class="center" style="height:75px" src='./../../../img/Screenshot-RDMkit-01-plan.png'/>
+
+<span class="footer-reference">**Zhou *et al.* (2023)**, DataPLAN: a web-based data management plan generator for the plant sciences, bioRxiv 2023.07.07.548147; doi: https://doi.org/10.1101/2023.07.07.548147 </span>
+
+https://dmpg.nfdi4plants.org
+
+![w:800](././../../../img/zhou2023-dataplan.png)
+
+---
+
+# The ARC ecosystem
+
+![w:850](./../../../img/ARC-ecosystem-07.drawio.png)
+
+---
+
+# The ARC ecosystem
+
+![w:850](./../../../img/ARC-ecosystem-09.drawio.png)
+
+---
+
+# The ARC ecosystem
+
+![w:850](./../../../img/ARC-ecosystem-10.drawio.png)
+
+---
+
+---
+
+# Contributors
+
+Slides presented here include contributions by
+
+- name: Dominik Brilhaus
+  github: https://github.com/brilator
+  orcid: https://orcid.org/0000-0001-9021-3197
+- name: Cristina Martins Rodrigues
+  github: https://github.com/CMR248
+  orcid: https://orcid.org/0000-0002-4849-1537
+- name: Martin Kuhl
+  github: https://github.com/Martin-Kuhl
+  orcid: https://orcid.org/0000-0002-8493-1077
diff --git a/...cs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.html b/...cs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.html