Start Your ARC Workshop Series

Session 01 - Introduction to the ARC (demo)
May 9th, 2023


Dominik Brilhaus - CEPLAS Data Science

CEPLAS collaborates with DataPLANT

CEPLAS collaborates with DataPLANT

Annotated Research Context (ARC)

What does an ARC look like?

What does an ARC look like?

What does an ARC look like?

What does an ARC look like?

What does an ARC look like?

What does an ARC look like?

left

First steps towards your ARC

You just received your data

Goal

  • 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 https://git.nfdi4plants.org/brilator/demo-arc

Invite collaborators to your ARC

https://git.nfdi4plants.org/brilator/demo-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

👩‍💻 Initiated an ARC


📂 Structured and ...


... annotated experimental data


🌐 Shared with collaborators

Resources

CEPLAS Data Science

Website: https://www.ceplas.eu/en/research/data-science-and-data-management/

DataPLANT (nfdi4plants)

Website: https://nfdi4plants.org/
Knowledge Base: https://nfdi4plants.org/nfdi4plants.knowledgebase/
DataHUB: https://git.nfdi4plants.org
GitHub: https://github.com/nfdi4plants

Acknowledgements

CEPLAS

Björn Usadel, Andrea Schrader, Hajira Jabeen (until 2021)

DataPLANT

Kaiserslautern: Timo Mühlhaus, Christoph Garth

  • Kevin Frey, Lukas Weil, Oliver Maus, Kevin Schneider
    (ARC Commander, Swate)
  • Martin Kuhl (Knowledge Base)
  • Jonas Lukasczyk (ARCitect)

Freiburg: Dirk von Suchodeletz

  • Jonathan Bauer, Marcel Tschöpe (DataHUB, Swobup)
  • Cristina Martins Rodrigues (Knowledge Base)

Five-Finger-Feedback

Contributors

Slides presented here include contributions by

Title slide to class

Source to slide(s)

../custom/bricks/ceplas-title-01.md

Source to slide(s)

../custom/bricks/ceplas-dataplant-collab.md

Source to slide(s)

../../bricks/ARC_DataCentricIntegration.md

Source to slide(s)

../../bricks/ARC_Structure_DataPLANT-1Folder_Structure.md

Source to slide(s)

../../bricks/ARC_Structure_DataPLANT-2Folder_Structure_ExperimentalData.md

Source to slide(s)

../../bricks/ARC_Structure_DataPLANT-3Folder_Structure_ExperimentalData_Images.md

Source to slide(s)

../../bricks/ARC_Structure_DataPLANT-4Folder_Structure_DataAnalysis-Computation.md

Source to slide(s)

../../bricks/ARC_Structure_DataPLANT-5Folder_Structure_DataAnalysis-Computation_Images.md

Source to slide(s)

../../bricks/ARC_Structure_DataPLANT-6Folder_Structure_MetadataAnnotation.md

Source to slide(s)

../../../units/lesson_022_ARC_structure_DataPLANT/lesson_022_ARC_structure_DataPLANT.md

Here you could address the general problems of the user. FAIRData_ActivationEnergy and FAIRData_ActivationEnergy_withDataPLANT would also be appropriate.

Source to slide(s)

../../bricks/User_Challenges.md

Here one could elaborate on the ARC structure as deeply as desired. In addition, Swate incl. ontology could be discussed here.

Source to slide(s)

../../bricks/FAIR-using-ARC.md

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT-1Storage-and-BackUp.md

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT-2Versioning.md

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT-3CollaborationAndAccessManagement.md

Here one could address repositories in general, but also ROC, Galaxy or Invenio.

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT-4MultipleContribution.md

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT-5ReferenceAndReuse.md

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT-6Publish.md

Source to slide(s)

../../bricks/BigPicture_ARC_DataPLANT.md

Source to slide(s)

../../../units/lesson_030_BigPicture_ARC_DataPLANT/lesson_030_BigPicture_ARC_DataPLANT.md

## 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 "https://demo-user:1_eznikmzxzARAbUxxnF@git.nfdi4plants.org/teaching/demo-arc_level0.git" ``` > 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>@git.nfdi4plants.org/<username>/<projectname>.git`

## Tools and software 📂 Explorer or Finder on your local computer <br> <img align="left" height=35px src='https://raw.githubusercontent.com/nfdi4plants/Branding/master/icons/Swate/Excel/Core/swate_c_40x40.png'/> DataPLANT's Excel-Plugin SWATE <br> 🌐 DataPLANT's [DataHUB](https://git.nfdi4plants.org/) <br> 👩‍💻 "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: - `https://git.nfdi4plants.org/` = DataHUB - `brilator/` = username @ DataHUB - `demo-arc` = name of the ARC @ DataHUB

## Check your progress at the DataHUB - Open your ARC at https://git.nfdi4plants.org/brilator/demo-arc/ and click the `commits` link below the project avatar - Or directly navigate to https://git.nfdi4plants.org/brilator/demo-arc/-/commits/main

*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

Source to slide(s)

../../../units/promotion_arc-demo/promotion_arc-demo.md

Source to slide(s)

../custom/bricks/links-resources.md

Source to slide(s)

../custom/bricks/acknowledgements.md

- Invite participants to give feedback - If feasible, collect transparently on a board or in a markdown pad, etc. # Five-Finger-Feedback ...was too short | I'm happy with... | I did not like at all ...| This idea or advice was good: ... | I really liked ... ---|---|---|---|--- ... | ... | ... | ... | ...

Source to slide(s)

../../../bricks/feedback_002_FiveFinger.md