From b3804dac3e4b5e678b12c50b51d315209ecaf836 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Tue, 14 Nov 2023 20:20:44 +0100 Subject: [PATCH] add ARC Club slides --- .../10-WelcomeIntro.html | 184 +++++----- .../10-WelcomeIntro.md | 19 +- .../20-ARC-ecosystem-demo.html | 169 +++++++++ .../20-ARC-ecosystem-demo.md | 284 +++++++++++++++ .../26-ARCitect-HandsOn.html | 246 +++++++++++++ .../26-ARCitect-HandsOn.md | 328 ++++++++++++++++++ .../42-DataHUB.html | 68 ++++ .../2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.md | 93 +++++ .../43-DataHUB-HandsOn.html | 189 ++++++++++ .../43-DataHUB-HandsOn.md | 217 ++++++++++++ .../2023-11-15_CEPLAS-ARC-Clubs/README.md | 7 +- .../hidden-index.md | 4 + .../2023-11-15_CEPLAS-ARC-Clubs/index.md | 6 +- 13 files changed, 1712 insertions(+), 102 deletions(-) create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.html create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.md create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.html create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.md create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.html create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.md create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.html create mode 100644 src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.md 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 index a2cd64c73..448199b8e 100644 --- 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 @@ -1,4 +1,4 @@ -Welcome and Intro
-

ARC Club

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+

The ARC Club


-November 15th, 2023 -Dominik Brilhaus, CEPLAS Data Science +

November 15th, 2023
+Dominik Brilhaus, CEPLAS Data Science

-
-

Welcome

+
+

Get-to-know

+
    +
  • Lab
    • +
  • CEPLAS / TRR / MibiNet / ?
    • +
  • Favorite lab assay
    • +
  • Used code / programming language before
    • +
  • Has an ORCID
    • +
-
-

House-keeping

-

Pad:

+
+

House-keeping

+

Pad: https://pad.hhu.de/ZG0nGuRyRo2D0T0vHnkTpQ?view

+
    +
  • take notes
    • +
  • ask questions
    • +
  • copy / paste links, etc.
    • +
-
-

Materials

+
+

Materials

Slides will be shared via DataPLANT knowledge base

-
-

Tentative agenda

+
+

Tentative agenda

-

Day 1

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
TimeTopics
09:30 - 10:45Intro to RDM and ARC
10:45 - 11:00Short break
11:00 - 12:00ARC Hands-on
12:30 - 13:30Lunch
13:00 - 15:30Data storage and sharing
15:30 - 16:00Wrap-up
+

Day 1

+
    +
  • Intro to ARC and demo
    • +
  • ARCitect Hands-on
    • +
  • Create your ARCs
    • +
  • DataHUB Features
    • +
-

Day 2

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
TimeTopics
09:30 - 10:30ARC Feedback session
10:30 - 10:45Short break
10:45 - 12:00ISA and Metadata
12:30 - 13:30Lunch
13:00 - 15:00Hands-on Swate
15:00 - 15:30ARC ecosystem: Additional features
15:30 - 16:00Wrap-up
+

Day 2

+
    +
  • ARC recap session
    • +
  • ISA and Metadata
    • +
  • Swate Hands-on
    • +
  • Annotate data in your ARC
    • +
-
-

Contributors

+
+

The ARC Club – Goals

+
    +
  • Move existing datasets into ARCs
    • +
  • Share them via the DataHUB
    • +
  • First few steps into ARCs
    • +
  • You or collaborators can pick them up from there
    • +
+
+
+

The ARC Club – Rules

+
    +
  1. You do not talk about ARC Club
    2. +
  2. You do not talk about ARC Club
    3. +
+
+
+

Rules: perfect is the enemy of good

+
    +
  • There is no perfect ARC
    • +
  • There is no complete ARC
    • +
  • The only bad ARCs are those that don't exist yet.
    • +
+
+

🚀 Let's get started, the rest is easy 🚀

+
+
+

Let's draw a typical lab workflow from your lab 📝

+
+
+

Resources

+

DataPLANT (nfdi4plants)

+

Website: https://nfdi4plants.org/
+Knowledge Base: https://nfdi4plants.org/nfdi4plants.knowledgebase/
+DataHUB: https://git.nfdi4plants.org

+

GitHub: https://github.com/nfdi4plants
+HelpDesk: https://helpdesk.nfdi4plants.org

+

💡 You can help us by raising issues, bugs, ideas...

+
+
+
+

Contributors

Slides presented here include contributions by

  • name: Dominik Brilhaus
    @@ -130,5 +122,5 @@

    Contributors

 \ No newline at end of file + \ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.md index 4d05a8cb6..488b26800 100644 --- a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.md +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/10-WelcomeIntro.md @@ -17,6 +17,7 @@ author:
+ November 15th, 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: + +--- + +# Resources + +### DataPLANT (nfdi4plants) + +Website: https://nfdi4plants.org/ +Knowledge Base: https://nfdi4plants.org/nfdi4plants.knowledgebase/ +DataHUB: https://git.nfdi4plants.org + + +GitHub: https://github.com/nfdi4plants +HelpDesk: https://helpdesk.nfdi4plants.org + +:bulb: You can help us by raising issues, bugs, ideas... --- diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.html b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.html new file mode 100644 index 000000000..a931ef77f --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.html @@ -0,0 +1,169 @@ +ARC Ecosystem Demo
+

The ARC ecosystem

+ +

A FAIR RDM journey along a (mutable) data life cycle

+
+
+
+

Data Stewardship between DataPLANT and the community

+

+
+
+

The research data life cycle

+
+

+

https://rdmkit.elixir-europe.org, CC BY 4.0

+
+
+

Annotated Research Context (ARC)

+

+
+
+

What does an ARC look like?

+

+
+
+

ARCs store experimental data

+

+
+
+

Computations can be run inside ARCs

+

+
+
+

ARCs come with comprehensive metadata

+

+
+
+

ARC builds on standards

+

+

https://isa-tools.org/ | https://www.commonwl.org/
+https://www.researchobject.org/ro-crate/ | https://git-scm.com

+
+
+
+

Collect

+

+
+
+

Process (e.g. annotate)

+ +

+
+
+

Analyse

+ +

+

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

+
+
+

Preserve

+ +

+

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

+
+
+

Preserve and publish

+ +

+

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

+
+
+

Share and collaborate

+

+
+
+

Reuse

+

+ +

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

+
+
+

Mutable data life cycle

+

+ +

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

+
+
+

Plan – ARC scale

+

+

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

+
+
+

Plan – proposal scale

+

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

+

https://dmpg.nfdi4plants.org

+

+
+
+

The ARC ecosystem

+

+
+
+

The ARC ecosystem

+

+
+
+

The ARC ecosystem

+

+
+
+
+

Contributors

+

Slides presented here include contributions by

+ +
+

- create study folder + - take a picture (add more demo pictures) +- create assay folder + - add fastq data

- annotate plant samples +- annotate rnaseq extraction

- run fastqc +- receive back results

1. Validation: CQC on each DataHUB commit +2. Publication: DOI

1. Validation: CQC on each DataHUB commit +2. Publication: DOI

- via ARC https://arcregistry.nfdi4plants.org/arcsearch +- via ISA https://arcregistry.nfdi4plants.org/isasearch

- Invite other (demo) account +- add notes from there

- **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)

\ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/20-ARC-ecosystem-demo.md new file mode 100644 index 000000000..21a8837c0 --- /dev/null +++ b/src/docs/teaching-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 +--- + + + +# The ARC ecosystem + + + + + + +### *A FAIR RDM journey along a (mutable) data life cycle* + +
+ +![bg fit](./../../../img/background_title_ceplas.drawio.svg) + +--- + +# Data Stewardship between DataPLANT and the community + +![w:880](././../../../img/DataPLANT-collaborationCEPLAS.drawio.png) + +--- + +# The research data life cycle + +
+ +![w:350](./../../../img/RDMkit-data_life_cycle_9.svg) + +https://rdmkit.elixir-europe.org, [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) + +--- + +# 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) + +https://isa-tools.org/ | https://www.commonwl.org/ +https://www.researchobject.org/ro-crate/ | https://git-scm.com + +--- + + + + + +--- + + +# Collect + +![width:800](./../../../img/ARC_fillWithData_experimental.png) + + + +--- + +# Process (e.g. annotate) + + + +![](./../../../img/Swate_metadataTemplates.png) + + + +--- + +# Analyse + + + +![w:800](./../../../img/tpj16474-fig-0005-m.jpg) + + 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 + +--- + +# Preserve + + + +![h:400](./../../../img/tpj16474-fig-0008-m-modified.png) + + 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 + +--- + +# Preserve and publish + + + +![h:400](././../../../img/tpj16474-fig-0008-m.jpg) + + 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 + +--- + +# Share and collaborate + +![w:700](./../../../img/ARC_DataSharing_Experts02_img1.png) + +--- + +# Reuse + +![w:800](./../../../img/tpj16474-fig-0001-m.jpg) + + + + 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 + +--- + +# **Mutable** data life cycle + +![w:700](./../../../img/tpj16474-fig-0006-m.jpg) + + + + 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 + +--- + +# Plan – ARC scale + +![w:800](./../../../img/tpj16474-fig-0007-m.jpg) + + 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 + + + +--- + +# Plan – proposal scale + +**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 + +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/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.html b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.html new file mode 100644 index 000000000..a402366ac --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.html @@ -0,0 +1,246 @@ +ARCitect hands-on
+

ARCitect hands-on

+
+
+

ARCitect installation

+

Please install version v0.0.10 of the ARCitect: https://github.com/nfdi4plants/ARCitect/releases/tag/v0.0.10

+

🔥 (released September 20th, 2023) 🔥

+
+
+

Download the demo data

+

https://nfdi4plant.sharepoint.com/:f:/s/Teaching/Eik7k-oJiMREgZ24kto7sIYBGxHmmZlS_Kzf7psk-5w-xg?e=u0sADd

+
+
+

Sort Demo data in an ARC

+ +

+
+
+

Open ARCitect

+
    +
  1. Login to DataHUB (1)
    +
    2. +
+
+
+

Initiate the ARC folder structure

+ +
    +
  1. Create a New ARC (2)
    2. +
  2. Select a location and name it TalinumPhotosynthesis
    3. +
+
+
+

Your ARC's name

+ +

💡 By default, your ARC's name will be used

+
    +
  • for the ARC folder on your machine
    • +
  • to create your ARC in the DataHUB at https://git.nfdi4plants.org/<YourUserName>/<YourARC> (see next steps)
    • +
  • as the identifier for your investigation
    • +
+

💡 Make sure that no ARC exists at https://git.nfdi4plants.org/<YourUserName>/<YourARC>. Otherwise you will sync to that ARC.

+

💡Don't use spaces in ARC's name

+
+
+

Add a description to your investigation

+

+
+
+

Add a contributor

+
+
+

Add a study

+

by clicking "Add Study" and entering an identifier for your study

+

Use talinum_drought as an identifier

+
+
+

Study panel

+

In the study panel you can add

+
    +
  • general metadata,
    • +
  • people, and
    • +
  • publications
    • +
  • data process information
    • +
+
+
+

Add an assay

+

by clicking "Add Assay" and entering an identifier for your assay

+

Add two assays with rnaseq and metabolomics as an identifier
+

+
+
+

Link your assay to a study

+

You can either

+
    +
  • link your new assay to an existing study in your ARC or
    • +
  • create a new one
    • +
+

Link your assays to your talinum_drought study

+
+
+

Add information about your assay

+

In the assay panel you can

+
    +
  1. link or unlink the assay to studies, and
    2. +
  2. define the assay's +
      +
    • measurement type
      • +
    • technology type, and
      • +
    • technology platform.
      • +
    +
    3. +
  3. add data process information
    4. +
+
+
+

Add protocols

+

You can either

+
    +
  • directly write a new protocol within the ARCitect or
    • +
  • import an existing one from your computer
    • +
+

+
+
+

Add protocols and datasets

+

In the file tree you can

+
    +
  • add a dataset and
    • +
  • protocols associated to that dataset.
    • +
+

💡 Add Dataset allows to import data from any location on your computer into the ARC.

+

⚠️ Depending on the file size, this may take a while. Test this with a small batch of files first.

+
+
+

Sort Demo Data to your ARC

+

💡 protocols can directly be imported via ARCitect

+

💡 to add multiple datasets folders, they have to be added manually via file browser

+
+
+

Login to the DataHUB

+

Click Login (1) in the sidebar to login to the DataHUB.

+

💡 This automatically opens your browser at the DataHUB (https://git.nfdi4plants.org) and asks you to login, if you are not already logged in.

+
+
+

Upload your local ARC to the DataHUB

+

From the sidebar, navigate to Versions (6)

+
+
+

Versions

+

The versions panel allows you to

+
    +
  • store the local changes to your ARC in form of "commits",
    • +
  • sync the changes to the DataHUB, and
    • +
  • check the history of your ARC
    • +
+
+
+

Connection to the DataHUB

+

If you are logged in, the versions panel shows

+
    +
  • your DataHUB's Full Name and eMail
    • +
  • the URL of the current ARC in the DataHUB https://git.nfdi4plants.org/<YourUserName>/<YourARC>
    • +
+
+
+

Check if your ARC is successfully uploaded

+
    +
  1. sign in to the DataHUB
    2. +
  2. Check your projects
    3. +
+
+
+

Your ARC is ready

+ +

👩‍💻 Initiated an ARC
+

+📂 Structured and ...
+

+ ... annotated experimental data
+

+🌐 Shared with collaborators

+
+
+
+

Received two emails from "GitLab" about a failed pipeline?

+

+

🔥 Don't worry 😄

+
+
+

Pipeline Failed

+ +
    +
  • +

    a "continuous quality control" (CQC) pipeline validates your ARC

    +
    • +
  • +

    This fails if one of the following metadata items is missing:

    +
    Investigation Identifier
+Investigation Title
+Investigation Description
+Investigation Person Last Name
+Investigation Person First Name
+Investigation Person Email
+Investigation Person Affiliation
+
    +
    • +
+
+
+

Pipeline Failed

+

If the pipeline has failed once, it is disabled by default

+
+
+

Reactivate the CQC pipeline

+ +

To reactivate it and let the DataHUB validate your ARC again:

+
    +
  1. navigate to CI/CD setting <arc-url>/-/settings/ci_cd
    2. +
  2. expand "Auto DevOps"
    3. +
  3. check box "Default to Auto DevOps pipeline"
    4. +
  4. Save changes
    5. +
+
+
+
+

Contributors

+

Slides presented here include contributions by

+ +
+

Demo dataset cannot be added via add dataset. Only individual files can be added, not multiple folders

\ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.md new file mode 100644 index 000000000..34986f33f --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/26-ARCitect-HandsOn.md @@ -0,0 +1,328 @@ +--- +marp: true +theme: marp-theme_dataplant-ceplas-ccby +paginate: true +license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)' +title: ARCitect hands-on +author: +- 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: Sabrina Zander + github: https://github.com/SabrinaZander + orcid: https://orcid.org/0009-0000-4569-6126 +--- + +# ARCitect hands-on + + + + +--- + +# ARCitect installation + +Please install version **v0.0.10** of the ARCitect: https://github.com/nfdi4plants/ARCitect/releases/tag/v0.0.10 + +:fire: (released September 20th, 2023) :fire: + +--- + +## Download the demo data + +https://nfdi4plant.sharepoint.com/:f:/s/Teaching/Eik7k-oJiMREgZ24kto7sIYBGxHmmZlS_Kzf7psk-5w-xg?e=u0sADd + +![bg right w:600](./../../../img/demo-data-download.png) + +--- + +# Sort Demo data in an ARC + +![bg right width:400](./../../../img/demo_data_screenshot.png) + +![width:900](./../../../img/ARC_fillWithData_experimental.png) + +--- + +# Open ARCitect + +1. Login to DataHUB (1) + ![bg right:40% w:250](./../../../img/ARCitect-help-Sidebar.drawio.svg) + +--- + +# Initiate the ARC folder structure + +![bg right:40% w:250](./../../../img/ARCitect-help-Sidebar.drawio.svg) + +1. Create a **New ARC** (2) +2. Select a location and name it **TalinumPhotosynthesis** + +--- + +# Your ARC's name + + + +💡 By default, your ARC's name will be used + - for the ARC folder on your machine + - to create your ARC in the DataHUB at `https://git.nfdi4plants.org//` (see next steps) + - as the identifier for your investigation + +💡 Make sure that no ARC exists at `https://git.nfdi4plants.org//`. Otherwise you will sync to that ARC. + +💡Don't use spaces in ARC's name + +![bg right:30% w:500](./../../../img/ARCitect_TalinumPhotosynthesis.png) + +--- + +# Add a description to your investigation + +![w:800](./../../../img/ARCitect_TalinumPhotosynthesis_InvestigationMetadata.png) + +--- + +# Add a contributor + + +![bg right w:500](./../../../img/ARCitect_TalinumPhotosynthesis_InvestigationPerson.png) + +--- + +# Add a study + +by clicking "Add Study" and entering an identifier for your study + +Use **talinum_drought** as an identifier + +![bg right w:500](./../../../img/ARCitect_TalinumPhotosynthesis_Study.png) + +--- + +# Study panel + +In the study panel you can add + +- general metadata, +- people, and +- publications +- data process information + +![bg right w:500](./../../../img/ARCitect_TalinumPhotosynthesis_StudyPanel.png) + +--- + + +# Add an assay + +by clicking "Add Assay" and entering an identifier for your assay + +Add two assays with **rnaseq** and **metabolomics** as an identifier +![bg right w:500](./../../../img/ARCitect_TalinumPhotosynthesis_Assay.png) + +--- + +# Link your assay to a study + +You can either +- link your new assay to an existing study in your ARC or +- create a new one + +Link your assays to your **talinum_drought** study + + +![bg right w:500](./../../../img/ARCitect_TalinumPhotosynthesis_Assay2.png) + +--- + +# Add information about your assay + +In the assay panel you can + +1. link or unlink the assay to studies, and +2. define the assay's + - measurement type + - technology type, and + - technology platform. +3. add data process information + +![bg right w:500](./../../../img/ARCitect_TalinumPhotosynthesis_AssayPanel.png) + +--- + +# Add protocols + +You can either +- directly write a **new protocol** within the ARCitect or +- import an existing one from your computer + +![w:800](./../../../img/arcitect-ARCPanel-protocol.png) + +--- + +# Add protocols and datasets + +In the file tree you can + - **add a dataset** and + - **protocols** associated to that dataset. + +:bulb: **Add Dataset** allows to import data from any location on your computer into the ARC. + +:warning: Depending on the file size, this may take a while. Test this with a small batch of files first. + + + +![bg right:40% w:400](./../../../img/arcitect-ARCPanel-assay03.png) + +--- + +# Sort Demo Data to your ARC + +💡 protocols can directly be imported via ARCitect + +💡 to add multiple datasets folders, they have to be added manually via file browser + +--- + +# Login to the DataHUB + +Click **Login** (1) in the sidebar to login to the DataHUB. + +:bulb: This automatically opens your browser at the DataHUB (https://git.nfdi4plants.org) and asks you to login, if you are not already logged in. + +![bg right:40% w:250](./../../../img/ARCitect-help-Sidebar.drawio.svg) + +--- + +# Upload your local ARC to the DataHUB + +From the sidebar, navigate to **Versions** (6) + +![bg right:40% w:250](./../../../img/ARCitect-help-Sidebar.drawio.svg) + +--- + +# Versions + +The versions panel allows you to +- store the local changes to your ARC in form of "commits", +- sync the changes to the DataHUB, and +- check the history of your ARC + +![bg right w:650](./../../../img/arcitect-VersionsPanel.png) + +--- + +# Connection to the DataHUB + +If you are logged in, the versions panel shows +- your DataHUB's *Full Name* and *eMail* +- the URL of the current ARC in the DataHUB `https://git.nfdi4plants.org//` + +![bg right w:650](./../../../img/arcitect-VersionsPanel.png) + +--- + +# Check if your ARC is successfully uploaded + +1. [sign in](https://auth.nfdi4plants.org/realms/dataplant/login-actions/registration?client_id=account&tab_id=4bQkU161waI) to the DataHUB +2. Check your projects + +--- + +# Your ARC is ready + + + +👩‍💻 Initiated an ARC +
+📂 Structured and ... +
+ ... annotated experimental data +
+🌐 Shared with collaborators + +![bg right width:400](./../../../img/demo_arc_screenshot.png) + +--- + +--- + +# Received two emails from "GitLab" about a failed pipeline? + +![w:600](./../../../img/cqc-error-email.png) + +:fire: Don't worry :smile: + +--- + +## Pipeline Failed + +![bg right w:700](./../../../img/cqc-error-badges.png) + +- a "continuous quality control" (CQC) pipeline validates your ARC +- This fails if one of the following metadata items is missing: + + ```bash + Investigation Identifier + Investigation Title + Investigation Description + Investigation Person Last Name + Investigation Person First Name + Investigation Person Email + Investigation Person Affiliation + ``` + +--- + +## Pipeline Failed + +If the pipeline has failed once, it is disabled by default + +![bg right w:500](./../../../img/cqc-error-email2.png) + +--- + +## Reactivate the CQC pipeline + + + +To reactivate it and let the DataHUB validate your ARC again: + + 1. navigate to CI/CD setting `/-/settings/ci_cd` + 2. expand "Auto DevOps" + 3. check box "Default to Auto DevOps pipeline" + 4. Save changes + +![bg right:60% w:600](./../../../img/cqc-activate-autodevops.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: Sabrina Zander + github: https://github.com/SabrinaZander + orcid: https://orcid.org/0009-0000-4569-6126 diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.html b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.html new file mode 100644 index 000000000..421b4c713 --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.html @@ -0,0 +1,68 @@ +DataPLANT DataHUB
+

DataPLANT DataHUB

+
+
+

ARC builds on standards + Git

+

+
+
+

The DataPLANT DataHUB – a GitLab Plus

+

+
+
+
+
+
+
+
+
+
+

Mutable data life cycle

+

+ +

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

+
+
+

Project management

+

+

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

+
+
+
+

Contributors

+

Slides presented here include contributions by

+ +
+

- Invite other (demo) account +- add notes from there

\ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.md new file mode 100644 index 000000000..d9bff62ec --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/42-DataHUB.md @@ -0,0 +1,93 @@ +--- +marp: true +theme: marp-theme_dataplant-ceplas-ccby +paginate: true +license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)' +title: DataPLANT DataHUB +author: +- 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 +--- + +# DataPLANT DataHUB + +--- + +# ARC builds on standards + Git + +![w:900](./../../../img/ARC_BuildsOnStandards2.png) + +--- + +# The DataPLANT DataHUB – a GitLab ***Plus*** + +![](./../../../img/DataHUB-GitLab.drawio.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq2.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq3.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq4.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq5.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq6.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq7.png) + +--- + +![bg cover](./../../../img/DataPLANT_BigPicture_seq8.png) + +--- + +# **Mutable** data life cycle + +![w:700](./../../../img/tpj16474-fig-0006-m.jpg) + + + + 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 + +--- + +# Project management + +![w:800](./../../../img/tpj16474-fig-0007-m.jpg) + + 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 + +--- + +--- + +# 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 diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.html b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.html new file mode 100644 index 000000000..0e701dd17 --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.html @@ -0,0 +1,189 @@ +DataHub Hands-On
+

DataHub Hands-On

+
+
+

Navigation Bar

+

+
    +
  1. navigate directly to the projects panel via the icon in the top-left (1)
    2. +
  2. open the hamburger Menu (2)
    3. +
  3. use the search field (3) to find ARCs, users and groups
    4. +
  4. open the avatar Menu (4)
    5. +
+
+
+

Hamburger Menu

+
    +
  1. From the hamburger menu (1) you can
    2. +
  2. navigate to the projects (2)
    3. +
  3. or groups (3) panels
    4. +
+
+
+

Avatar Menu

+
    +
  1. In the avatar menu (1) you can
    2. +
  2. find your profile name and user name (2),
    3. +
  3. navigate to the user settings (3)
    4. +
  4. or sign out (4) of the DataHUB.
    5. +
+
+
+

Projects Panel

+

+
    +
  1. Choose a tab (1) to see only your ARCs, or explore other publicly available ARCs.
    2. +
  2. The main panel (2) lists all ARCs
    3. +
  3. Here you can also see, the visibility level (3), and
    4. +
  4. your permission or role (4) for the listed ARC.
    5. +
  5. You can create a New Project in the top-right corner (5).
    6. +
+
+
+

ARC Panel

+

The ARC Panel is the main working area for your ARC.

+

+
+
+

ARC Panel – sidebar

+ +
    +
  1. access the project information (1), e.g. invite members to the ARC
    2. +
  2. follow the progress of your ARC repository (2),
    3. +
  3. organize tasks in issue lists and boards (3),
    4. +
  4. take notes in a wiki to your ARC (4),
    5. +
  5. adapt the settings (5) of the ARC.
    6. +
+
+
+

ARC Panel – main panel

+ +
    +
  1. see the ARC's name and visibility level (6),
    2. +
  2. follow the ARC's commit history (7),
    3. +
  3. see files contained in your ARC just like on your computer (8),
    4. +
  4. add new files or directories (9), and
    5. +
  5. download or clone your ARC (10).
    6. +
+
+
+

Collaborate and share

+

+
+
+

Invite collaborators

+
    +
  • Unless changed, your ARC is set to private by default.
    • +
  • To collaborate, you can invite lab colleagues or project partners to your ARC by following the steps on the subsequent slides.
    • +
  • To get started sign in to the DataHUB and open the ARC you want to share.
    • +
+
+
+
    +
  1. Click on Project Information in the left navigation panel
    2. +
+

fit

+
+
+
    +
  1. Click on Members
    2. +
+

fit

+
+
+
    +
  1. Click on Invite members
    2. +
+

fit

+
+
+
    +
  1. Search for potential collaborators
    2. +
+

fit

+
+
+
    +
  1. Select a role
    2. +
+

fit

+
+
+

Choosing the proper role

+ +

Guests
+Have the least rights. They will not be able to see the content of your ARC (only the wiki page).

+

Reporters
+Have read access to your ARC. This is recommended for people you ask for consultancy.

+

Developers
+The choice for most people you want to invite to your ARC. Developers have read and write access, but cannot maintain the project on the DataHUB, e.g. inviting others.

+

Maintainers
+Gives the person the same rights as you have (except of removing you from your own project). This is recommended for inviting PIs or group leaders allowing them to add their group members for data upload or analysis to the project as well.

+

A detailed list of all permissions for the individual roles can be found here

+
+
+

Congratulations!

+
You have just shared your ARC with a collaborator.
+ +

+
+
+

Version control

+
    +
  • Commit history
    • +
+
+
+

Project Management

+
    +
  • Issues
    • +
+
+
+

ARCs come with their own wiki space

+
    +
  • directly associated to your ARC
    • +
  • same access rights as your ARC
    • +
  • share meeting minutes or ideas with collaboration partners
    • +
  • keep ARC clean of files that are not considered "research data"
    • +
+
+
+
+

Contributors

+

Slides presented here include contributions by

+ +
+
\ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.md new file mode 100644 index 000000000..df807f588 --- /dev/null +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/43-DataHUB-HandsOn.md @@ -0,0 +1,217 @@ +--- +marp: true +theme: marp-theme_dataplant-ceplas-ccby +paginate: true +license: '[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)' +title: DataHub Hands-On +author: +- 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 +--- + +# DataHub Hands-On + +--- + +# Navigation Bar + +![](./../../../img/datahub-navbar.drawio.svg) + +1. navigate directly to the [projects panel](./../../../../../../DataHUB-Manual/datahub-Manual/datahub-projectsPanel.html) via the icon in the top-left (1) +2. open the [hamburger Menu](#hamburger-menu) (2) +3. use the search field (3) to find ARCs, users and groups +4. open the [avatar Menu](#avatar-menu) (4) + +--- + +# Hamburger Menu + +1. From the hamburger menu (1) you can +2. navigate to the [projects](./../../../DataHUB-Manual/datahub-projectsPanel.html) (2) +3. or [groups](datahub-groupsPanel.html) (3) panels + +![bg right w:500](./../../../img/datahub-hamburgerMenu.drawio.svg) + +--- + +# Avatar Menu + +1. In the avatar menu (1) you can +2. find your profile name and user name (2), +3. navigate to the [user settings](./../../../DataHUB-Manual/datahub-userSettings.html) (3) +4. or sign out (4) of the DataHUB. + +![bg right w:500](./../../../img/datahub-avatarMenu.drawio.svg) + +--- + +# Projects Panel + +![](./../../../img/datahub-projectsPanel.drawio.svg) + +1. Choose a tab (1) to see only your ARCs, or explore other publicly available ARCs. +2. The main panel (2) lists all ARCs +3. Here you can also see, the visibility level (3), and +4. your permission or role (4) for the listed ARC. +5. You can create a **New Project** in the top-right corner (5). + +--- + +# ARC Panel + +The ARC Panel is the main working area for your ARC. + +![w:1000](./../../../img/datahub-ARC-overview.drawio.svg) + +--- + +# ARC Panel – sidebar + + + +![bg right w:600](./../../../img/datahub-ARC-overview.drawio.svg) + +1. access the project information (1), e.g. invite members to the ARC +2. follow the progress of your ARC repository (2), +3. organize tasks in issue lists and boards (3), +4. take notes in a wiki to your ARC (4), +5. adapt the [settings (5) of the ARC](datahub-ARCSettings.html). + +--- + +# ARC Panel – main panel + + + +![bg right w:600](./../../../img/datahub-ARC-overview.drawio.svg) + +6. see the ARC's name and visibility level (6), +7. follow the ARC's commit history (7), +8. see files contained in your ARC just like on your computer (8), +9. add new files or directories (9), and +10. download or clone your ARC (10). + +--- + +# Collaborate and share + +![w:650](./../../../img/ARC_DataSharing_Experts02_img1.png) + +--- + +# Invite collaborators + +* Unless changed, your ARC is set to private by default. +* To collaborate, you can invite lab colleagues or project partners to your ARC by following the steps on the subsequent slides. +* To get started [sign in](https://auth.nfdi4plants.org/realms/dataplant/login-actions/registration?client_id=account&tab_id=4bQkU161waI) to the DataHUB and open the ARC you want to share. + +--- + +1. Click on **Project Information** in the left navigation panel + +![fit w:1050](./../../../img/datahub_members_seq2.png) + +--- + +2. Click on **Members** + +![fit w:1050](./../../../img/datahub_members_seq3.png) + +--- + +3. Click on **Invite members** + +![fit w:1050](./../../../img/datahub_members_seq4.png) + +--- + +4. Search for potential collaborators + +![fit w:1050](./../../../img/datahub_members_seq5.png) + +--- + +5. Select a role + +![fit w:1050](./../../../img/datahub_members_seq6.png) + +--- + +# Choosing the proper role + + + +Guests +Have the least rights. They will not be able to see the content of your ARC (only the wiki page). + +Reporters +Have **read access** to your ARC. This is recommended for people you ask for consultancy. + +Developers +The choice for most people you want to invite to your ARC. Developers have **read and write access**, but cannot maintain the project on the DataHUB, e.g. inviting others. + +Maintainers +Gives the person the same rights as you have (except of removing you from your own project). This is recommended for inviting PIs or group leaders allowing them to add their group members for data upload or analysis to the project as well. + +*A detailed list of all permissions for the individual roles can be found [here](https://docs.gitlab.com/ee/user/permissions.html)* + +--- + +#
Congratulations!
+
You have just shared your ARC with a collaborator.
+ + + +![](./../../../img/ARC_Sharing_img1.png) + +--- + + +# Version control + +- Commit history + +--- + +# Project Management + +- Issues + +--- + +# ARCs come with their own wiki space + +- directly associated to your ARC +- same access rights as your ARC +- share meeting minutes or ideas with collaboration partners +- keep ARC clean of files that are not considered "research data" + +![bg right w:600](./../../../img/datahub-wiki.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 diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/README.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/README.md index 623b9f386..6de41cce1 100644 --- a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/README.md +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/README.md @@ -6,8 +6,11 @@ date: 2023-11-15 ## See website locally -1. Execute `npm run fornax` -2. Open http://127.0.0.1:8080/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs +1. Execute +```bash +npm run fornax +``` +3. Open http://127.0.0.1:8080/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/index.html ## Batch-compile marp slide decks to html diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/hidden-index.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/hidden-index.md index bd3b11fdc..598d2058d 100644 --- a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/hidden-index.md +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/hidden-index.md @@ -8,3 +8,7 @@ add sidebar: _sidebars/mainSidebar.md ## Slide decks - WelcomeIntro +- ARC-ecosystem-demo +- ARCitect-HandsOn +- DataHUB +- DataHUB-HandsOn diff --git a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/index.md b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/index.md index 01ec62fb3..69f053d8d 100644 --- a/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/index.md +++ b/src/docs/teaching-materials/disseminations/2023-11-15_CEPLAS-ARC-Clubs/index.md @@ -9,15 +9,15 @@ add sidebar: _sidebars/mainSidebar.md Here you can find the slides prepared for the November / December 2023 CEPLAS ARC Clubs +## Announcement + - Announcement ## Slide decks -### Day 1 - - WelcomeIntro -### Day 2 + :warning: Links are not permanent. Slides may move elsewhere or be updated. We do our best to keep the knowledge base up-to-date – so you will find all relevant information here.