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
User Journey
ARC specification
ARC Commander
QuickStart
QuickStart (Experts)
Swate
QuickStart
Walk-through
Best Practices For Data Annotation
DataHUB
DataPLAN
Ontology Service Landscape
ARC Commander Manual
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 Manual
Installation - Windows
Installation - macOS
Installation - Linux
QuickStart
QuickStart - Videos
ARCmanager Manual
What is the ARCmanager?
How to use the ARCmanager
Swate Manual
Swate Installation
Excel Browser
Excel Desktop
Windows – installer
Windows – manually
macOS – manually
Organization-wide
Core Features
Annotation tables
Building blocks
Building Block Types
Adding a Building Block
Using Units with Building Blocks
Filling cells with ontology terms
Advanced Term Search
Templates
File Picker
Expert Features
Contribute Templates
ISA-JSON
DataHUB Manual
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
Data publications
Passing Continuous Quality Control
Submitting ARCs with ARChigator
Track publication status
Use your DOIs
Guides
ARC User Journey
Create your ARC
ARC Commander QuickStart
ARC Commander QuickStart (Experts)
ARCitect QuickStart
Annotate Data in your ARC
Annotation Principles
ISA File Types
Best Practices For Data Annotation
Swate QuickStart
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
Working with large data files
Adding external data to the ARC
ARCs in Enabling Platforms
Publication to ARC
Troubleshooting
Git Troubleshooting
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
CEPLAS ARC Trainings – Spring 2024
MibiNet CEPLAS DataPLANT Tool-Workshops
Frequently Asked Questions
last updated at 2022-07-06
What is Markdown?
- Markdown is a lightweight markup language
- Other markup languages: HyperText Markup Language (HTML), Extensible Markup Language (XML), LaTeX
- WYSIWYG: "What You See Is What You Get
- You literally write out, what you want the text to look like
- File extensions:
.md
or .markdown
- Official markdown website: https://daringfireball.net/projects/markdown/
Note: No worries, this is not about learning HTML. The following is just an example to show the idea of markup.
In HTML:
<html>
<body>
<h3>headline level 3</h3>
<h4>headline level 4</h4>
</body>
</html>
In Markdown:
### headline level 3
#### headline level 4
Rendered output:
headline level 3
headline level 4
In HTML:
<ul>
<li>List item 1</li>
<li><strong>List item 2 in bold</strong></li>
</ul>
In Markdown:
- List item 1
- **List item 2 in bold**
Rendered output:
- List item 1
- List item 2 in bold
Why Markdown?
- simple, plain text format
- no hassle with formatting
- Worry about content, not layout.
- Most benefits of LaTeX, but simpler
- easy-to-read, easy-to-write
- intuitively human-readable
- machine-actionable, convertible
- independent
- open source
- You only need a text editor
- No need for "word processor programs"
- Microsoft Word, WordPad, macOS Pages, Google Docs, LibreOffice Writer
- reusable
- text is not stuck in formats or layouts
- extendible
- many programs and tools work with markdown
Is there anything markdown can't do?
- Beautiful, perfectly designed documents or slide shows
- Reminder: "WYSIWYG"
- Theming, customization, special formatting, design is hard(ly possible)
- Use a word processor (or LaTeX 😉 )
- Collaboration on documents (e.g. reviewing manuscripts)
- comments, suggestions, discuss changes, text highlighting
Markdown <> Code & Data Management?
- Works perfectly with (text based) version-control (-> git)
- Many GitHub / GitLab features are based on MD
- README.md, issues, wiki pages, discussions and comments
- referencing files and folders, e.g. in a README.md
- Structuring and commenting code supported by IDEs, e.g.
- Jupyter Notebooks ~ markdown-commented python scripts
- RMarkdown ~ markdown-commented R scripts
Implementations and variants
Markdown can be used in many programming languages, platforms and frameworks, incl.:
Note: There are different flavors to how and what is "interpreted",
e.g. not every markdown parser understands
- bold html text
- emojis 🚲, 🍻, ⛺
- or footnotes
Converting markdown files
In case you want to provide your markdown document in another file format, converters help you.
The top recommendation: Pandoc.
Note: pandoc conversion to pdf depends on a LaTeX Installation on your system.
If you run into issues, see https://pandoc.org/installing.html for details and recommendations.
Use pandoc to convert your...
pandoc README.md -o markdown_intro.html # ... markdown to .html
pandoc README.md -o markdown_intro.pdf # ... markdown to .pdf
pandoc README.md -o markdown_intro.docx # ... markdown to .docx
pandoc -t slidy -s --slide-level=2 --metadata pagetitle=markdown_intro README.md -o markdown_intro_slides.html # ... markdown to html slides
Real-time collaboration
Although markdown is not perfect for collaboration on documents (e.g. manuscripts), there are occasions where online collaboration in markdown format comes in very handy (meetings with people that understand MD, code-intensive classes, etc.).
Tutorials and resources
Recommended VS code extensions
There are many markdown extensions available for Visual Studio Code.
These support you in
Hands-on markdown tutorial
mostly (adapted) from https://daringfireball.net/projects/markdown/dingus
Software
Try writing a markdown document, using either
- an online markdown editor (e.g. https://demo.hedgedoc.org/new),
- the GitHub or GitLab IDE to create / adapt the
README.md
, or
- (advanced) your favorite text-editor that supports markdown.
Basic Syntax
Phrase Emphasis
*This is italic*
_This is also italic_
**This is bold**
__This is also bold__
# Header 1
## Header 2
###### Header 6
Lists
Ordered, without paragraphs:
1. Item 1
2. Item 2
4. Item 3
Note the "4." in md
Unordered, with paragraphs:
- A list item.
- Bar
You can nest them:
- Abacus
* answer
* Bubbles
1. bunk
2. bupkis
- BELITTLER
3. burper
Note: indentation matters
Blockquotes
```
> Email-style angle brackets
> are used for blockquotes.
> > And, they can be nested.
> #### Headers in blockquotes
>
> - You can quote a list.
> - Etc.
```
Code Spans
```
- `<code>` spans are delimited by backticks.
- You can include literal backticks like `` `this` ``.
```
Code Blocks
```
This is a code block
```
Horizontal Rules
Three or more dashes or asterisks:
---
* * *
- - - -
Manual Line Breaks
End a line with two or more spaces:
Roses are red,
Violets are blue.
Links
- Inline:
An [example](http://url.com/ "Title")
- Reference-style labels (titles are optional):
An [example][id]. Then, anywhere else in the doc, define the link:
[id]: http://example.com/ "Title"
Images
![alt text](./../img/ARC_BuildsOnStandards1.png "This is an ARC")
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
.