Block 3 – ARCitect and hands-on

ARCitect installation

Please install the latest version of the ARCitect: https://github.com/nfdi4plants/ARCitect

(released September 20th, 2023)

Download the demo data

git clone "https://demo-user:1_eznikmzxzARAbUxxnF@git.nfdi4plants.org/teaching/demo-arc_level0.git"

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 (at least one) 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 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

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

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. Click on Members

3. Click on Invite members

4. Search for potential collaborators

5. Select a role

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!

Your ARC is ready

Initiated an ARC


Structured and ...


... annotated experimental data


Shared with collaborators

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