Start Your ARC Workshop Series

(Preparation for) Session 03


Dominik Brilhaus - CEPLAS Data Science

Checklist ARC data annotation hands-on

  • ✅ Install Swate on your computer
  • ✅ Prepare an ARC with your data

Swate Installation

Please follow these instructions to install the latest version of Swate.

Part 1: Prepare your ARC

Your fresh ARC folder

  1. 💻 Create a new folder, which you want to initialize as an ARC.
  2. 💻 Open the command line inside the folder or navigate via command line to that folder.

For example:

mkdir -p ~/Desktop/workshop-arcs/my-arc
cd ~/Desktop/workshop-arcs/my-arc

ARC initialization

Initialize your ARC by executing

arc init

Upload your local ARC to the DataHUB

In order to connect your local ARC with a remote ARC, you can specify the remote address with the flag -r followed by the URL of the remote ARC

arc sync -r https://git.nfdi4plants.org/<username>/my-arc

Successful ARC synchronization

Check if the upload was successful by visiting your ARC at the respective URL in your browser.

Part 2: Adding subfolders for your data

Preparation

Before you can fill your ARC, let's revise your data.

  • What is my investigation?
  • What is my study?
  • Which assay did I perform?
    • What is my (raw) dataset?
    • What protocols did I use?

💡 It might help to have this info ready in a text file. In particular, try to think about useful identifiers for investigation, study and assay.

ISA investigation

The ISA investigation (-i) workbook allows you to record administrative metadata of your project. Add the isa.investigation.xlsx workbook including an identifier to your ARC with

arc investigation create --identifier <YourInvestigationID>

💡 Avoid using spaces in the identifier. Use underscores and capital letters instead.

ISA studies and assays

The ISA study (s) and ISA assay (a) workbooks allow you to annotate your experimental data.

Adding a study

Add a study folder with the isa.study.xlsx workbook including an identifier to your ARC with

arc s add --studyidentifier <YourStudyID>

Adding an assay

Add an assay folder with the isa.assay.xlsx workbook including an identifier to your ARC with

arc assay add --studyidentifier <YourStudyID> --assayidentifier <YourAssayID>

💡 An assay must be linked to a study. If a study does not exist, it will be created automatically in this step.

ISA studies and assays

The ARC Commander adds subdirectories to the studies and assays folders. Your ARC should, look similar to this now:

These steps can be repeated to add as many studies and assays as needed. Accordingly, more subdirectories will be added

Sync your ARC to the DataHUB

To save the changes, sync the ARC to the DataHUB including a message (-m).

arc sync -m "initiate arc structure"

🌐 Check your ARC in the DataHUB.

Part 3: Structure your data

Start adding your data to the ARC

Try to place your resources, datasets and protocols for each study and assay in the respective folders.

💡 This part will likely require some iteration. 🗣️ Talk to us.

  • You might need to add new studies and assays or revise your overall structure during the process
  • Sometimes you might not immediately find a suitable position for your data

Part 4: 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

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  1. Click on Members

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  1. Click on Invite members

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  1. Search for potential collaborators

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  1. Select a role

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Choosing the proper role

Guest
Have the least rights. 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!

You have just shared your ARC with a collaborator.

Contributors

Slides presented here include contributions by

Title slide to class

Source to slide(s)

../../bricks/datahub_invite-collaborators.md

Source to slide(s)

../../bricks/datahub_choose-collaborator-role.md

Source to slide(s)

../../bricks/datahub_congrats-for-sharing.md