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)

Initiate the ARC folder structure

  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/<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. define the assay's
    • measurement type
    • technology type, and
    • technology platform.
  3. add data process information

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. Check your projects

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. expand "Auto DevOps"
  3. check box "Default to Auto DevOps pipeline"
  4. Save changes

Contributors

Slides presented here include contributions by

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