First steps towards your ARC

Dominik Brilhaus - May 10, 2023

You just received your data


  • Structure,
  • Annotate, and
  • Share your experimental data.

Structure your data

Annotate your data

Collaborate and share

Sync your ARC to the DataHUB

arc sync -f -r

Invite collaborators to your ARC

Using the ARC Commander to setup an ARC

Initiate the ARC folder structure

arc init

Add metadata structure

arc investigation create -i TalinumPhotosynthesis
arc study add -s talinum_drought
arc assay add -s talinum_drought -a rnaseq
arc assay add -s talinum_drought -a metabolomics

Your ARC is ready

Your ARC is ready

πŸ‘©β€πŸ’» Initiated an ARC

πŸ“‚ Structured and ...

... annotated experimental data

🌐 Shared with collaborators

--- ## Tutor prep: - change `<username>` in `arc sync` steps - make sure no `demo-arc` exists at given URL or adapt URL in sync steps - download the folder with unstructured sample data ```bash git clone "" ``` > no access needed, "read_registry" token is part of command > Note: If you want to provide another dataset for download. > 1. Create a new DataHUB project with the data. > 2. Create an access token only for that project with role "maintainer" and scopes "read_repository". > 3. Adapt the URL `https://<tokenname>:<token><username>/<projectname>.git`

--- ## Tools and software πŸ“‚ Explorer or Finder on your local computer <br> <img align="left" height=35px src=''/> DataPLANT's Excel-Plugin SWATE <br> 🌐 DataPLANT's [DataHUB]( <br> πŸ‘©β€πŸ’» "Terminal" or "command prompt" on your local computer

1. Fill study characteristics (completely manually) 2. Fill assay parameters (by template, copy paste metadata from sheet, link files by picker) 3. Fill assay parameters (by json import, link files by picker)

:bulb: The URL decomposed: - `` = DataHUB - `brilator/` = username @Β DataHUB - `demo-arc` = name of the ARC @ DataHUB

--- ## Check your progress at the DataHUB - Open your ARC at and click the `commits` link below the project avatar - Or directly navigate to

*Create and navigate to a new folder*

```bash mkdir ~/Desktop/demo-arc; cd ~/Desktop/demo-arc ```

--- ## Outlook 1. Data analysis: add workflows and runs (scripts + external data) 2. Iterative and reproducible data analysis: add runs (CWL) 3. Publish your ARC and get a DOI