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.

Agenda

In this tutorial, we will:

1. Video Lectures
   1. How it Works
2. Enabling Video
   1. Writing Good Captions
   2. Enable the Video
3. Voices
4. How it works: In Detail
5. 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.

Punctuation

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

Abbreviations

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.

E.g.

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.

Voices

There are multiple voices available, see the following list:

By default a random voice is chosen every time the video is rebuilt (only whenever a change is made to that slide deck.) We do this to ensure a good diversity of genders and nationalities in the audio samples.

However, if you have a preferred voice, you can set that permanently for that video, add the following metadata to the top of your slide deck:

voice:
  id: Lupe
  lang: es-US
  neural: true

The above voice example is specific to Spanish language content, hence not being represented in the first list.

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 ari.sh which does the following:

   • make video is run which runs bin/ari-make.sh
   • This builds PDFs for any slides which have changed
   • And runs ./bin/ari.sh with the PDF, the original Slides, and where the mp4 should be saved.
     • In ./bin/ari.sh
     • It extracts metadata from the tutorial (title, authors, etc.)
     • It builds a ‘script’, a json document with blocks for every line of the speaker notes that were in the slides.
     • Those get converted into mp3 files by AWS Polly (or MozillaTTS), one per slide.
     • The PDFs get turned into a series of PNG images
     • We take the timings of the mp3 files together with the json ‘script’ to write out webvtt / srt subtitles which get embedded into the video, and supplied next to it.
     • editly is used to knit together the PNGs + mp3s with appropriate delay

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 github.com/jhudsl/ari/ 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.

Conclusion

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Thanks to the GTN, videos are easy to add

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

Frequently Asked Questions

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Citing this Tutorial

1. Helena Rasche, Adding auto-generated video to your slides (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/contributing/tutorials/slides-with-video/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{contributing-slides-with-video,
author = "Helena Rasche",
	title = "Adding auto-generated video to your slides (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/contributing/tutorials/slides-with-video/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	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}
}

                   

Developing GTN training material

This tutorial is part of a series to develop GTN training material, feel free to also look at:

1. Contributing with GitHub via command-line
2. Overview of the Galaxy Training Material
3. Creating Interactive Galaxy Tours
4. Contributing with GitHub via its interface
5. Generating PDF artefacts of the website
6. Tools, Data, and Workflows for tutorials
7. Teaching Python
8. Running the GTN website online using GitHub CodeSpaces
9. Design and plan session, course, materials
10. GTN Metadata
11. Running the GTN website online using GitPod
12. Adding auto-generated video to your slides
13. Including a new topic
14. Adding Quizzes to your Tutorial
15. Principles of learning and how they apply to training and teaching
16. Updating diffs in admin training
17. Running the GTN website locally using the command line
18. Creating a new tutorial
19. Single Cell Publication - Data Plotting
20. FAIR Galaxy Training Material
21. Single Cell Publication - Data Analysis
22. Creating content in Markdown
23. Creating Slides

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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