20-ARCitect-HandsOn.md

marp	theme	paginate	license	title	author
true	marp-theme_dataplant-ceplas-mibinet-ccby	true	[CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)	ARCitect Hands-on	name github orcid Dominik Brilhaus https://github.com/brilator https://orcid.org/0000-0001-9021-3197 name github orcid Cristina Martins Rodrigues https://github.com/CMR248 https://orcid.org/0000-0002-4849-1537 name github orcid Sabrina Zander https://github.com/SabrinaZander https://orcid.org/0009-0000-4569-6126

ARCitect Hands-on

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ARCitect installation

Please install version v0.0.31 (or later) of the ARCitect: https://github.com/nfdi4plants/ARCitect/releases/latest

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Download the demo data

https://uni-duesseldorf.sciebo.de/s/C7ms3QA6q7OZnU2

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Sort Demo data in an ARC

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Open ARCitect

1. Login to DataHUB (1)
2. Select git.nfdi4plants.org as Host

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Initiate the ARC folder structure

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

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Your ARC's name

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💡 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.

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Add a description to your investigation

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Add a contributor

• you could also add the contacts directly via ORCID

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Add a study

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

Use talinum_drought as an identifier

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Study panel

In the study panel you can add

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

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Add an assay

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

Add two assays with rnaseq and metabolomics as an identifier

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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

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Add information about your assay

In the assay panel you can define the assay's

• measurement type
• technology type, and
• technology platform

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Add protocols

You can either

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

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Add protocols and datasets

In the file tree you can

• import dataset files or folders and
• protocols associated to that dataset.

💡 Import 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.

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Sort Demo Data to your ARC

💡 protocols and multiple datasets can directly be imported via ARCitect

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Explorer

The Explorer (6) button directly opens your ARC locally

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Commit panel (7)

You have to commit changes before you can upload to the DataHUB

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If you are logged in, the Commit panel shows

• your DataHUB's Full Name and eMail

It allows you to

• track changes of the ARC with git
• add a commit message
• use different branches

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History panel (9)

In the History panel you can inspect your ARCs history with all commits

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Upload your local ARC to the DataHUB

From the sidebar, navigate to DataHUB Sync (8)

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DataHUB Sync

The DataHUB Sync panel allows you to

• sync the changes to the DataHUB: Push
• sync from the DataHUB: Pull, and
• change the Remote for the synchronization

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Check if your ARC is successfully uploaded

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

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Your ARC is ready

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👩‍💻 Initiated an ARC
📂 Structured and ...

... annotated experimental data
🌐 Shared with collaborators

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

🔥 Don't worry 😄

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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

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Pipeline Failed

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

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Reactivate the CQC pipeline

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

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