Fundamentals

Introduction

Research Data Management

FAIR Data Principles

Metadata

Data Sharing

Data Publications

Data Management Plan

Version Control & Git

Public Data Repositories

Persistent Identifiers

Implementation within DataPLANT

Annotated Research Context

ARC Commander

Swate - a workflow annotation tool for Excel

DataHUB

Training & Tutorials

QuickStart on ARCs

ARC Commander QuickStart

Swate QuickStart

Best practices for data annotation

ARC Commander QuickStart

last updated at 2022-08-05

This document is work in progress. If you experience any inconsistencies, have questions or would like to suggest additions, please feel free to contact us or open an issue in our Helpdesk.

We are very happy that you chose our tools and infrastructure to create and share your own ARCs. In this QuickStart we focus on how to use the "ARC Commander" to store and share your data.

Environment and setup The command line

Windows Powershell

echo "hello - I am a code block" Required software

Note: If this is your first time using git on this computer, you need to set your git user name and email address. These are needed for displaying them on the git commits. You can update the settings with

git config --global user.name <your_name> git config --global user.email <your_email> arc --version arc --help

ARC Commander help menu

ARC initialization
  1. Create and navigate to a local folder, which you want to initialize as an ARC.
mkdir ~/Desktop/QuickStart; cd ~/Desktop/QuickStart
  1. Initialize your ARC by executing
arc init
  1. This will create the general ARC folder structure:

arc init

Adding metadata 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 i create -i QuickStartInvestigation ISA studies and assays

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

  1. Add an isa.study.xlsx workbook including an identifier to your ARC with
arc s add -s QuickStartStudy
  1. Add an isa.assay.xlsx workbook including an identifier to your ARC with
arc a add -s QuickStartStudy -a QuickStartAssay

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

subdirectories

  1. Place the data for each assay in the respective dataset folder.
Sharing your ARC DataPLANT registration and access

In case you are not a member of DataPLANT yet, please visit sign up. Afterwards, you will be granted access to DataPLANT’s DataHUB. The DataHUB allows you to share your ARCs with registered lab or project partners.

After successful registration, create and set an access token for ARC Commander synchronization using

arc remote accesstoken get -s https://git.nfdi4plants.org

A window within your browser will open, asking for your DataPLANT Log In. In case you are already logged in, the browser will directly display a Success message to you:

ARC synchronization
  1. Synchronize your ARCs with the DataHUB using the command
arc sync
  1. If you did not connect your local ARC with a remote one so far, you can specify the remote address with the flag -r followed by an URL, e.g.,
arc sync -r https://gitlab.nfdi4plants.de/martinkuhl/QuickStart
  1. In case you want to create a new remote repository at this URL, it needs to be assembled as the following example:
# https://gitlab.nfdi4plants.de/<YourUserName>/<YourARC>
  1. If no repository exists under the given URL, the ARC Commander will produce an error ensuring that you spelled the URL correctly. To force synchronization, use
arc sync -f

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

Note: Alternatively, you can first create a new blank repository in the DataHUB by clicking "New project/repository" in the plus drop down menu of the navigation bar on top. Afterwards, you can sync your local ARC to the respective repository by adapting the URL to the newly generated one.

Setting a git user

Some users might want to use different signatures for different repositories, e.g. for developing software on GitHub and working on ARCs on DataPLANT's DataHUB. Besides your global git configuration, you can store the information you want to use for editing ARCs within the ARC Commander config:

arc config set -g -n "general.gitname" -v "Name of choice" arc config set -g -n "general.gitemail" -v "Email of choice"

To transfer the information from the global ARC Commander config to the local git config of the ARC use

arc config setgituser Invite collaborators

You can invite lab-colleagues or project partners to join your ARC for collaboration. While inside your ARC on the DataHUB, click on Project information -> Members in the left navigation panel. Search for registered researchers and select a role for each individually. These roles come along with different rights.
Briefly:

Note: A detailed usage instruction for the ARC Commander can be found here.

The Minimalist's ARC-QuickStart

Voila! You are ready to follow these few steps to create a minimal ARC sharable via DataPLANT's DataHUB:

  1. Visit the DataHUB, create a new repository and copy the URL to your clipboard.
  2. Replace the <variables> in the following code block with your information and execute it in your command line.
# Create and navigate to your ARC folder mkdir <YourARC> cd <YourARC> # Setup the ARC structure with one study and one assay arc init arc i create -i <YourInvestigation> arc a add -s <YourStudy> -a <YourAssay> arc sync -f -r https://gitlab.nfdi4plants.de/<YourUserName>/<YourARC> -m "initialize ARC structure"

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
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