Adding auto-generated video to your slides

Authors: orcid logoAvatarHelena Rasche
  • How can we add auto-generated video?

  • How does it work?

  • What do I need to do to make it optimal for viewers?

  • Adding a video to a set of slides

Time estimation: 20 minutes
Supporting Materials:
Last modification: Oct 18, 2022
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License The GTN Framework is licensed under MIT

Video Lectures

Based on the work by Delphine Larivière and James Taylor with their COVID-19 Lectures we have implemented a similar feature in the Galaxy Training Network.


In this tutorial, we will:

  1. Video Lectures
    1. How it Works
  2. Enabling Video
    1. Writing Good Captions
    2. Enable the Video
  3. How it works: In Detail
  4. Conclusion

How it Works

We wrote a short script which does the following:

Locally and in production:

  • Extracts a ‘script’ from the slides. We extract every presenter comment in the slidedeck, and turn this into a text file.
  • Every line of this text file is then narrated by Amazon Polly (if you have money) or MozillaTTS (free).
  • The slide deck is converted to a PDF, and then each slide is extracted as a PNG.
  • Captions are extracted from the audio components.
  • The narration is stitched together into an mp3
  • The images are stitched together into an mp4 file
  • The video, audio, and captions are muxed together into a final mp4 file

In production

  • We use Amazon Polly, paid for by the Galaxyproject
  • The result is uploaded to an S3 bucket

Enabling Video

We have attempted to simplify this process as much as possible, but making good slides which work well is up to you.

Writing Good Captions

Every slide must have some narration in the presenter notes. It does not make sense for students to see a slide without commentary. For each slide, you’ll need to write presenter notes in full, but short sentences.

Sentence Structure

Use simple and uncomplex sentences whenever possible. Break up ideas into easy to digest bits. Students will be listening to this spoken and possibly reading the captions.

2021-05-01 There used to be a limit of ~120 characters per sentence, but this is no longer an issue. We now break up sentences which are too long in the captions and show them over multiple timepoints. So if you need to write a really long sentence, you can, but we still advise to simplify sentences where possible.

Captions per Slide

Every slide must have some speaker notes in this system, NO exceptions.


Sentences should end with punctuation like . or ? or even ! if you’re feeling excited.


These are generally fine as-is. (e.g. e.g./i.e. is fine as-is, RNA is fine, etc.) Make sure abbreviations are all caps though.

Good This role deploys CVMFS.

“Weird” Names

In the captions you will want to teach the GTN how to pronounce these words by editing bin/ari-map.yml to provide your definition.


Word Pronunciation
SQLAlchemy SQL alchemy
FastQC fast QC
nginx engine X
gxadmin GX admin
/etc / E T C

The same applies to the many terms we read differently from how they are written, e.g. ‘src’ vs ‘source’. Most of us would pronounce it like the latter, even though it isn’t spelt that way. Our speaking robot doesn’t know what we mean, so we need to spell it out properly.

So we write the definition in the bin/ari-map.yml file.

Other Considerations

(Written 2020-12-16, things may have changed since.)

Be sure to check the pronunciation of the slides. There are known issues with heteronyms, words spelt the same but having different pronunciation and meaning. Consider “read” for a classic example, or “analyses” for one that comes up often in the GTN. “She analyses data” and “Multiple analyses” are pronounced quite differently based on their usage in sentences. See the wiktionary page for more information, or the list of English heteronyms you might want to be aware of.

This becomes an issue for AWS Polly and Mozilla’s TTS which both don’t have sufficient context sometimes to choose between the two pronunciations. You’ll find that “many analyses” is pronounced correctly while “multiple analyses” isn’t.

Oftentimes the services don’t understand part of speech, so by adding adjectives to analyses, you confuse the engine in to thinking it should be the third person singular pronunciation. This is probably because it only has one or two words of context ahead of the word to be pronounced.

Enable the Video

Lastly, we need to tell the GTN framework we would like videos to be generated.

Hands-on: Enable video
  1. Edit the slides.html for your tutorial
  2. Add video: true to the top

That’s it! With this, videos can be automatically generated.

How it works: In Detail

  1. We take our markdown slides, e.g. topics/introduction/tutorials/galaxy-intro-short/slides.html
  2. In order for them to be processed, slides must have an annotation saying video: true in the header metadata, and then ‘speaker notes’ (everything after the ??? before the —)
  3. This is turned into our ‘plain text slides’ which just renders the markdown a bit more nicely (example)
  4. Then we run which does the following:

All of this is run on cron by .github/workflows/video.yml which handles building all of these videos and then later uploading them to s3.

Many of the scripts internally are prefixed with ari, we named our internal version after which inspired it, but we wanted a version that would be more closely tied to the GTN and integrate with our infrastructure nicely, so we ended up writing our own.


Key points
  • Thanks to the GTN, videos are easy to add

  • Be mindful of your captions. Short sentences are good!

Frequently Asked Questions

Have questions about this tutorial? Check out the tutorial FAQ page or the FAQ page for the Contributing to the Galaxy Training Material topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help Forum


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Citing this Tutorial

  1. Helena Rasche, Adding auto-generated video to your slides (Galaxy Training Materials). Online; accessed TODAY
  2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

author = "Helena Rasche",
title = "Adding auto-generated video to your slides (Galaxy Training Materials)",
year = "",
month = "",
day = ""
url = "\url{}",
note = "[Online; accessed TODAY]"
	doi = {10.1371/journal.pcbi.1010752},
	url = {},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol} Computational Biology}


Congratulations on successfully completing this tutorial!
Developing GTN training material
This tutorial is part of a series to develop GTN training material, feel free to also look at:
  1. Creating a new tutorial
  2. Contributing with GitHub via command-line
  3. Creating Slides
  4. Overview of the Galaxy Training Material
  5. Tools, Data, and Workflows for tutorials
  6. Running the GTN website online using GitPod
  7. GTN Metadata
  8. Generating PDF artefacts of the website
  9. Updating diffs in admin training
  10. Principles of learning and how they apply to training and teaching
  11. Running the GTN website locally
  12. Design and plan session, course, materials
  13. Teaching Python
  14. Contributing with GitHub via its interface
  15. Adding auto-generated video to your slides
  16. Including a new topic
  17. Creating content in Markdown
  18. Adding Quizzes to your Tutorial
  19. Creating Interactive Galaxy Tours