ARCitect Hands-on

ARCitect installation

Please install version v0.0.31 (or later) of the ARCitect:

Download the demo data

Sort Demo data in an ARC

Open ARCitect

  1. Login to DataHUB (1)
  2. Select 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<YourUserName>/<YourARC> (see next steps)
  • as the identifier for your investigation

💡 Make sure that no ARC exists at<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


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

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

TODO - more to remote? - add history panel - add Swate alpha examples in ARCitect ??? - check linking studies and assays

TODO show connected assays

TODO more to remote?