Home
Fundamentals
Research Data Management
FAIR Data Principles
Metadata
Ontologies
Data Sharing
Data Publications
Data Management Plan
Version Control & Git
Public Data Repositories
Persistent Identifiers
Electronic Lab Notebooks (ELN)
DataPLANT Implementations
Annotated Research Context
ARC specification
ARC Commander
Swate
MetadataQuiz
DataHUB
DataPLAN
Ontology Service Landscape
Manuals
ARC Commander
Setup
Git Installation
ARC Commander Installation
Windows
MacOS
Linux
ARC Commander DataHUB Access
Before we start
Central Functions
Initialize
Clone
Connect
Synchronize
Configure
Branch
ISA Metadata Functions
ISA Metadata
Investigation
Study
Assay
Update
Export
ARCitect
Installation - Windows
Installation - macOS
Installation - Linux
QuickStart
QuickStart - Videos
ARCmanager
What is the ARCmanager?
Connect to your DataHUB
View your ARCs
Create new ARCs
Add new studies and assays
Upload files
Add metadata to your ARCs
Swate
QuickStart
QuickStart - Videos
Annotation tables
Building blocks
Building Block Types
Adding a Building Block
Filling cells with ontology terms
Advanced Term Search
File Picker
Templates
Contribute Templates
ISA-JSON
DataHUB
Overview
User Settings
Generate a Personal Access Token (PAT)
Projects Panel
ARC Panel
Forks
Working with files
ARC Settings
ARC Wiki
Groups Panel
Create a new user group
CQC Pipelines & validation
Find and use ARC validation packages
Data publications
Passing Continuous Quality Control
Submitting ARCs with ARChigator
Track publication status
Use your DOIs
Guides
ARC User Journey
Create your ARC
ARCitect QuickStart
ARCitect QuickStart - Videos
ARC Commander QuickStart
ARC Commander QuickStart (Experts)
Annotate Data in your ARC
Annotation Principles
ISA File Types
Best Practices For Data Annotation
Swate QuickStart
Swate QuickStart - Videos
Swate Walk-through
Share your ARC
Register at the DataHUB
DataPLANT account
Invite collaborators to your ARC
Sharing ARCs via the DataHUB
Work with your ARC
Using ARCs with Galaxy
Computational Workflows
CWL Introduction
CWL runner installation
CWL Examples
CWL Metadata
Recommended ARC practices
Syncing recommendation
Keep files from syncing to the DataHUB
Managing ARCs across locations
Working with large data files
Adding external data to the ARC
ARCs in Enabling Platforms
Publication to ARC
Troubleshooting
Git Troubleshooting & Tips
Contribute
Swate Templates
Knowledge Base
Teaching Materials
Events 2023
Nov: CEPLAS PhD Module
Oct: CSCS CEPLAS Start Your ARC
Sept: MibiNet CEPLAS Start Your ARC
July: RPTU Summer School on RDM
July: Data Steward Circle
May: CEPLAS Start Your ARC Series
Start Your ARC Series - Videos
Events 2024
TRR175 Becoming FAIR
CEPLAS ARC Trainings – Spring 2024
MibiNet CEPLAS DataPLANT Tool-Workshops
TRR175 Tutzing Retreat
Frequently Asked Questions
last updated at 2023-06-29
About this guide
This guide tries to describe the current way to prepare and contribute slide decks via the knowledge base.
🚧 The mechanism to prepare and render slide decks in the knowledge base is currently under construction. So this guide is incomplete.
Before we start
Creating a marp slide decks
Creation of slide decks is based on marp
- Create a new markdown file
test-slides.md
- Add
marp: true
to the YAML frontmatter of the file.
- Add content to the file just as you would do for a markdown text document.
- Add
---
(horizontal lines) as slide breaks
🚧 Repo file structure and where to store the slide deck is under construction
View / export result:
- preview via VS Code preview (cmd + k, v)
- export via VS Code command
Marp: Export Slide Deck
(to html or PDF) or right-click the Marp symbol in the top-right corner while in edit mode of the markdown file
Speaker notes
Can be added as markdown comments.
<!-- markdown notes -->
These will appear in presenter mode (html) or in PDF (if "markdown.marp.pdf.noteAnnotations": true
is added to the .vscode/settings.json
)
Presentation mode
- export to html (opens in browser) and hit the presentation icon
Default slide size
1280 x 720
Pro
- easy to adapt (from existing md content)
- customizable (requires css and / or html skills)
- can directly render draw.io images
Con
- theme needs to be linked (also) via .vscode/settings.json
Tips
https://www.hashbangcode.com/article/seven-tips-getting-most-out-marp
Themes
Custom themes based on CSS are currently stored in src/docs/teaching-materials/style/
VS Code Marp Settings
In order to work with the VS Code marp extension (i.e. preview and export slides to pdf, html, etc.), you might want to add the following to the gitignored VS code settings (.vscode/settings.json
) of this repo. If the file does not exist, please create it.
{
"markdown.marp.themes": [
"src/docs/teaching-materials/style/dataplant_marp-theme.css",
"src/docs/teaching-materials/style/dataplant_marp-theme-CMR.css",
"src/docs/teaching-materials/style/dataplant_marp-theme-Intro.css",
"src/docs/teaching-materials/style/marp-theme_dataplant-ceplas-ccby.css"
],
"markdown.marp.enableHtml": true,
"markdown.marp.exportType": "html",
"markdown.marp.pdf.noteAnnotations": false
}
Debugging
- If images are not properly linked, marp cannot parse and render them in pdf or html.
- the VS Code extension will not throw a warning and just ouput an empty (figure-less) slide
- There's an easy way to find the missing / incorrect image links on the html version of your marp slides using your browser described here:
https://github.com/marp-team/marp/discussions/257
Example Slide deck
Please check out the rendered example slide deck.
And compare it to its source markdown.
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
.