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

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.

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.
Starting the ARCitect for the first time.

When starting the 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.

Every time you start the ARCitect, you are asked to accept incoming network connections.
This enables communication with the DataHUB.

Head to the ARCitect’s GitHub release page.
Download the Linux AppImage ARCitect-x.x.x.AppImage.
(optional) If you run Ubuntu 22.04 you need to download an additional library. Ubuntu 22.04 can’t run AppImage files without the not natively installed FUSE library. To fix this, install the necessary library. To do this you need root permissions.
Requires root permission
```
sudo apt install libfuse2
```
Make the ARCitect executable.

You need to make the downloaded AppImage executable before you can run it. You can use the user interface or the command line to do this.
- User Interface
- Command Line
1. Open the folder where the AppImage is currently saved (likely in Downloads).
2. (optional) Move the file to a location where you want it saved.
3. Right-click the file and select properties.
4. Go to the “permissions” tab and tick the field “execute”.
5. Now double-clicking the AppImage should start the ARCitect.
1. Open a terminal.
2. Move to the directory where you have saved your AppImage (e.g. Downloads).
  Terminal window
  cd Downloads
3. Make the file executable (use the appropriate name of the file).
  Terminal window
  chmod u+x ARCitect-x.x.x.AppImage
4. Now double-clicking the AppImage or running the following command (with the appropriate file name) should start the ARCitect.
  Terminal window
  ./ARCitect-x.x.x.AppImage

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”
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 Violoas 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.