Create an ARC

So, where do I start? What is an ARC? And how do I create one?

An ARC represents an entire investigation. At the top level, it includes directories named “studies,” “assays,” “workflows,” and “runs,” along with an investigation metadata table that holds all administrative metadata.

It follows a very specific structure to be easily readable by machines 🤖. While it can be created by hand it is faster to use some tooling!

ARCitect installation

The easiest way to create a new ARC is via ARCitect.

ARCitect installation

If ARCitect is not yet installed on your computer,

please follow these instructions to install ARCitect

ARCitect depends on Git and Git LFS.
The ARCitect installer for Windows includes both tools automatically.
On macOS and Linux, Git and Git LFS have to be installed separately.

Check git installation

To check, that Git and Git LFS are installed on your computer, open a new command prompt or terminal and execute the following two commands. These should display the installed version. If not, follow the installation instructions.

Open a command prompt or terminal
Check the installed Git version via
Terminal window
```
git --version
```
Recommended Git version ≥ 2.32.0
Check the installed Git LFS version via
Terminal window
```
git-lfs --version
```
Recommended Git LFS version ≥ 3.6.1

Head to the ARCitect’s GitHub release page.
Under “Assets” Download the latest release for Windows (ARCitect-x.x.x-win.zip).
In Windows Explorer, open the folder where you downloaded the ARCitect.
Unzip (Right click ➞ Extract All..) the folder (ARCitect-x.x.x-win.zip). You can move this folder to another location (e.g. Program files).
Start the ARCitect, by clicking the ARCitect application.
Once started, you see a Windows Defender warning. To proceed, click More info and then Run anyway.
Windows Defender Firewall further asks you to allow network communication. This enables communication with the DataHUB.

You might have to select the app from your taskbar.

Git Installation

Download the Git installer for Windows from https://git-scm.com.
Open the installer and follow the installation instructions
During the installation, make sure to include Git LFS (Large File Support)

Open a Terminal
(Optional, if homebrew is not yet installed:) Install the package manager homebrew via
Terminal window
```
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
```
Install Git via homebrew with
Terminal window
```
brew install git
```
Install Git LFS via homebrew with
Terminal window
```
brew install git-lfs
```
Initialize Git LFS via
Terminal window
```
git lfs install
```

Open a Terminal
Update the package manager apt via
Terminal window
```
sudo apt update
```
Install Git via apt with
Terminal window
```
sudo apt-get install git
```
Install Git LFS via apt with
Terminal window
```
sudo apt-get install git-lfs
```
Initialize Git LFS via
Terminal window
```
git lfs install
```

ARCitect Installation

Head to the ARCitect’s GitHub release page.
Download the macOS installer ARCitect-x.x.x.dmg.
Double-click the installer ARCitect-x.x.x.dmg and move the app to your Applications folder.

Unidentified developer

When starting ARCitect for the first time, you are warned about an unidentified developer.

Please navigate to the Privacy & Security panel in your System Settings to Open Anyway.

Accept incoming network connections

Every time you start the ARCitect, you are asked to accept incoming network connections.

This enables communication with the DataHUB.

Git Installation

Download the Git installer for Windows from https://git-scm.com.
Open the installer and follow the installation instructions
During the installation, make sure to include Git LFS (Large File Support)

Open a Terminal
(Optional, if homebrew is not yet installed:) Install the package manager homebrew via
Terminal window
```
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
```
Install Git via homebrew with
Terminal window
```
brew install git
```
Install Git LFS via homebrew with
Terminal window
```
brew install git-lfs
```
Initialize Git LFS via
Terminal window
```
git lfs install
```

Open a Terminal
Update the package manager apt via
Terminal window
```
sudo apt update
```
Install Git via apt with
Terminal window
```
sudo apt-get install git
```
Install Git LFS via apt with
Terminal window
```
sudo apt-get install git-lfs
```
Initialize Git LFS via
Terminal window
```
git lfs install
```

ARCitect Installation

Install additional dependencies via
Terminal window
```
sudo apt-get update
sudo apt-get install libgtk-3-0 libnotify4 xdg-utils libsecret-1-0
```
On some linux distributions you have to run sudo apt --fix-broken install afterwards.
Head to the ARCitect’s GitHub release page.
Download the Linux DEB package ARCitect-x.x.x_amd64.deb.
Install ARCitect
Terminal window
```
sudo dpkg -i ./ARCitect-x.x.x_amd64.deb
```
Start the ARCitect via
Terminal window
```
arcitect
```

Create a new ARC

ARCitect

Start the ARCitect app.
In the sidebar on the left, click on New ARC.
Select a location and name for your ARC.

To keep it simple, I call my ARC “AthalianaColdStressSugar”
Tip
- Use a short acronym
- Avoid spaces and special characters in your ARC’s name
- Avoid administrative metadata (name, data, etc.)
- Use a combination of keywords maybe grant number
ARCitect creates the base ARC folder on your computer and opens it right away.
- DirectoryAthalianaColdStressSugar
  - studies
  - assays
  - workflows
  - runs
  - isa.investigation.xlsx
The isa.investigation.xlsx is not displayed inside ARCitect, but can be accessed by clicking on “AthalianaColdStressSugar” (in Viola’s example).

Your ARC's name

By default, your ARC’s name will be used:

For the ARC folder on your computer.
As the investigation identifier.