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 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 Workflows Manual CWL Introduction CWL runner installation CWL Examples CWL Metadata 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 Work with your ARC Using ARCs with Galaxy 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 Contribute Swate Templates Knowledge Base Teaching Materials Slides DataPLANT Annotated Research Context Videos Start Your ARC Series 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 Frequently Asked Questions

Introduction to Markdown

last updated at 2022-07-06 What is 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:

Why Markdown? Is there anything markdown can't do? Markdown <> Code & Data Management? 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

Converting markdown files

In case you want to provide your markdown document in another file format, converters help you. The top recommendation: Pandoc.3

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

  1. an online markdown editor (e.g. https://demo.hedgedoc.org/new),
  2. the GitHub or GitLab IDE to create / adapt the README.md, or
  3. (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__ Headers # 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")

alt text


  1. Integrated development environments

  2. I am a footnote

  3. https://pandoc.org/ "Pandoc"

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 .
Contribution Guide 📖
✏️ Edit this page