Fundamentals
Research Data Management
FAIR Data Principles
Metadata
Ontologies
Data Sharing
Data Publications
Data Management Plan
Version Control & Git
Public Data Repositories
Persistent Identifiers
Implementation within DataPLANT
Annotated Research Context
User Journey
ARC Commander
QuickStart
QuickStart (experts)
Swate
QuickStart
Walk-through
Best Practices For Data Annotation
DataHUB
DataPLAN
ARC Commander Manual
Setup
Installing Dependencies
Configure Git
Installing the ARC Commander
Windows
MacOS
Linux
DataHUB Access
Before we start
Central Functions
Initialize
Clone
Connect
Synchronize
Configure
Branch
ISA Metadata Functions
ISA Metadata
Investigation
Study
Assay
Update
Export
Swate Manual
Setup
Installing Swate
Browser
Desktop, via installer (beta-stage)
Desktop, manually (recommended)
MacOS
Organization-wide
Core Features
Annotation tables
Building blocks
Building Block Types
Adding a Building Block
Using Units with Building Blocks
Filling cells with ontology terms
Advanced Term Search
Templates
Contribute Templates
File Picker
Expert Features
ISA-JSON
Frequently Asked Questions
Teaching Materials
DataPLANT Overview
Big Picture
ARC structure
ARC Demo
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
- Most of this Quickstart (especially the section ARC initialization) is based on the command line (Windows: powershell; Linux and Mac: terminal).
- The following picture shows exemplarily how to open a powershell on windows by entering powershell into the explorer path:

- Text formatted as code blocks represents commands to copy/paste into the command line:
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>
You can check the configuration with
git config --global --get-regexp user
arc --version
arc --help

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

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
Note: 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.
- Add an isa.study.xlsx workbook including an identifier to your ARC with
arc s add -s QuickStartStudy
- 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.
- The ARC Commander will add a subdirectories to the studies and assays folder. 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. Multiple assays can be grouped in a study when the same StudyIdentifier is used.
- 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, setup your machine for smooth ARC synchronization using the ARC Commander
Allow git to store credentials on your machine.
Windows
git config --global credential.helper cache
or
git config --global credential.helper store
MacOS
git config --global credential.helper osxkeychain
Linux
git config --global credential.helper store
Create and set an access token
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
- Synchronize your ARCs with the DataHUB using the command
arc sync
- 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
- 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>
- 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

- 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:
- Guests: 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.

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