ARCitect Hands-on

ARCitect installation

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

Download the demo data

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

Sort Demo data in an ARC

Open ARCitect

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

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.

Add a description to your investigation

Add a contributor

• you could also add the contacts directly via ORCID

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 define the assay's

• measurement type
• technology type, and
• technology platform

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

• 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.

Sort Demo Data to your ARC

protocols and multiple datasets can directly be imported via ARCitect

Explorer

The Explorer (6) button directly opens your ARC locally

Commit panel (7)

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

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

History panel (9)

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

Upload your local ARC to the DataHUB

From the sidebar, navigate to DataHUB Sync (8)

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

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