Block 3 – ARCitect Hands-on

October 5th, 2023

Dominik Brilhaus, CEPLAS Data Science

Check-in

Registration

Did everyone sign-up at the DataHUB?

ARCitect installation

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

(released September 20th, 2023)

Download the demo data

https://nfdi4plant.sharepoint.com/:f:/s/Teaching/Eik7k-oJiMREgZ24kto7sIYBGxHmmZlS_Kzf7psk-5w-xg?e=u0sADd

You just received your data

Goal

• Structure,
• (Annotate, and)
• Share your experimental data.

We'll talk about data annotation later

Open the ARCitect

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:

1. for the ARC folder on your machine
2. to create your ARC in the DataHUB at https://git.nfdi4plants.org/<YourUserName>/<YourARC> (see next steps)
3. 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.

Avoid spaces in your ARC's name

Add a description and title to the investigation

1. Click on the ARC's name
2. Add a title (e.g. "Talinum Photosynsthesis")
3. Add a description
4. Click "Update" to save your changes

Add contributors

In the section "People" click "ADD PERSON" to add at least one contributor

Add contributor details

For each person that you add, make sure to add

• First Name
• Last Name
• Email
• Affiliation

Add a study

by clicking "Add Study" and entering talinum_drought as identifier for the study

Study panel

In the study panel you can add

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

Add a protocol to the study

Click "Add Protocol" in the sidebar to add a protocol to the study

Adding protocols

You can either

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

Transfer the protocol information

From the demo data, transfer the lab notes stored in plant_material.txt to the talinum_drought study.

Add an assay to the ARC

Click "Add Assay" in the sidebar

Name and link the assay

1. Enter rnaseq as the identifier
2. Link the assay to the study talinum_drought

Add information about the 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 information about the assay

1. Add the following information:
   • Measurement Type: Gene Expression Analysis
   • Technology type: Next Generation Sequencing
   • Technology platform: Illumina HiSeq 2500
2. Click "Update" to save your changes

Add protocols and datasets

In the file tree you can

• add a dataset and
• protocols associated with that dataset

Import the demo dataset to the ARC

1. Cick "Add Dataset"
2. Select the *.fastq.gz files from the demo data

Import the protocols

From the demo data, import the lab notes related to the rnaseq assay:

• RNA_extraction.txt
• Illumina_libraries.txt
• NGS_SampleSheet.xlsx

Collaborate and share

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.

Versions: Connection to the DataHUB

To communicate with the DataHUB, 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>

Upload your ARC to the DataHUB

1. Enter a "commit message" to shortly describe the changes to your ARC
2. Click "COMMIT" to save your changes locally
3. Click "UPLOAD" to upload your ARC to the DataHUB

Check whether your ARC was uploaded successfully

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

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!

Add the remaining data

1. Add another assay (metabolomics)
   1. Add the protocols
   2. Add the dataset
2. Go to the Versions panel
   1. Add a "commit message"
   2. Upload your changes to the DataHUB

Check the progress of your ARC

1. Navigate to Versions
2. Check the History panel at the bottom

Your ARC is ready

Initiated an ARC


Structured and ...


... annotated experimental data


Shared with collaborators

DataHUB

Deleting an ARC

1. Click on Settings in the sidebar of your ARC
2. Navigate to the general (1) settings
3. In the advanced section (4) you can delete your ARC

Follow your progress in the DataHUB

1. Open your ARC in the DataHUB
2. In the sidebar on the left, navigate to Repository → Commits
3. There you find a chronological list of syncing messages together with who synced and when

Undo latest changes

4. Click on the latest (i.e. uppermost) commit.
5. In the top-right corner select Revert from the drop-down menu Options.

Undo latest changes

6. Un-check the box "Start a new merge request with these changes".
7. Click "Revert"

Update your local ARC

If your ARC has changed in the DataHUB (by yourself or collaborators), you need to update your "local" version of the ARC.

1. Navigate to Versions
2. Click "Download"

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