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Check the code (.rst) source to see how these examples are written in restructured text.

Many of the examples Writing your documentation using sample data

Where possible, you want write documentation instructions to be general enough for users can follow along with their own data. To help do this, you can use the sample data admonition to intersperse sample data-specific instructions into your generic instructions.

To do this, start your documentation with a description and where possible, a citation of the data:

Sample data

How to use provided sample data

In this guide, we will use an RNA-Seq dataset (“Zika infected hNPCs”). This experiment compared human neuroprogenetor cells (hNPCs) infected with the Zika virus to non-infected hNPCs. You can read more about the experimental conditions and methods here. Where appropriate, a note (in this orange colored background) in the instructions will indicate which options to select to make use of this provided dataset.

Sample data citation: Yi L, Pimentel H, Pachter L (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLOS ONE 12(4): e0175744. 10.1371/journal.pone.0175744

Then, as you have instructions, intersperse the sample data .. admonition

  1. First, enter the cutoff value for your dataset

    Sample data

    “Zika infected hNPCs” dataset:

    Enter 30

  2. Continue with next step…

Other admonitions

There are several admonitions you can use, but tip and warning are the most common for our documentation.


If you don’t see a desired species/genome contact us to have it added


When naming your samples and conditions, avoid spaces and special characters (e.g. !#$%^&/, etc.). Also be sure to be consistent with spelling.

Buttons and keyboard combinations

Where it adds clarity you can use this text to add buttons:

  1. Click Cancel to continue
  2. Press Control + P to print your result
  3. Fix the CyVerse_launch link in custom_url.txt to use this button to launch a quicklaunch link in the DE (the embed HTML the DE generates may not render properly in RTD)

Detail expand questions

You can have questions by using .. admonition:: Question and .. admonition:: Answer. Just make sure you pay attention to spacing as below.


  1. Test your reader’s knowledge with a question


Give them an answer

  1. Test your reader’s knowledge with a question


Give them an answer

Embed video

You can embed responsive YouTube videos:


Images should only be used when necessary.

Choose an image size that works for your page:

Too big kitten

Better size:

Right-size kitten

Images should have a 1px black border:

Right-size kitten w border