galaxyproject
New tutorial: "Phylogenetics: back to basics"
Hello GTN team,
We’re submitting a new tutorial “Phylogenetics: back to basics” for review and hope that you’ll find it suitable for the GTN. It’s based on a live workshop run by Australian BioCommons and Professor Michael Charleston from the University of Tasmania.
This workshop was very popular and we’re keen to share it via the GTN so that more people can take advantage of it.
This tutorial takes a slightly different approach to other GTN tutorials in that it’s not a “how-to guide”. Instead it is aimed at giving a better understanding of the principles of phylogenetics and how the methods work. It uses tools that are (mostly) available in Galaxy to demonstrate these principles. We think it makes a great companion to other evolution-themed GTN tutorials.
A couple of things we need your help with:
We’ve submitted the data to the GTN Zenodo community and are waiting on approval before we can add a link. We’d like to centre align the videos but this requires adding some new settings for the whole website. Can you help us with this?
Given that it’s close to the Christmas break we understand that reviews will take longer than usual. We’re taking a break too and look forward to hearing your feedback in the new year!
You can contact us through GitHub or by email.
Many thanks,
Michael Charleston ([email protected]) Adam Taranto ([email protected]) Melissa Burke ([email protected])
We’ve submitted the data to the GTN Zenodo community and are waiting on approval before we can add a link.
you should be able to add the link now, the approval is only for it to show up in the GTN page in zenodo, the record should still be accessible even if it isn't yet in the Gtn zenodo community.
We’d like to centre align the videos but this requires adding some new settings for the whole website. Can you help us with this?
this is possible yes
Hi @Adamtaranto, welcome to the GTN! (A longer response now that I have my laptop available.)
it’s not a “how-to guide”. Instead it is aimed at giving a better understanding of the principles of phylogenetics and how the methods work
In general this looks great, it doesn't have to be as hands on as other tutorials, we're happy to accept excellent learning resources like these. They're achieving similar didactic purposes through different methods, that's fantastic. This looks like an excellent resource and we'll be very glad to have it on the GTN (maybe it's an era of more aussie biocommons contributions? which would be very exciting for us!)
The videos are the main point of discussion from our side. We heavily discourage the use of videos, you'll note they aren't present in essentially any other tutorials with few exceptions. We do this because the most accessible video is still less accessible than a well marked up HTML page.
I've taken a look at the videos you've linked in the tutorial, it's great to see you've got manual captions on them, that is a baseline requirement for us. That said, they're not maybe what one would refer to as high production slides? there's little to no animation, it's mostly talking through a slide deck (which is great and useful as-is!!!) So, given the GTN's position on slide deck accessibility and that aspect of the existing videos, I'd like to propose a more accessible alternative where you can retain the videos, and we can offer something that will work for all learners, rather than just the sighted ones:
If you would be willing to turn the slide decks from those videos, into GTN slide decks, then from our side we'll contribute a widget/box that you can use within the tutorial, that will give learners the option to choose their preferred in which to consume the tutorial; a video, the gtn remark.js slide deck, or the "plain text" slides which don't require javascript, and help you link to the correct places in each of those resources. (I wish I could offer here an automated method for doing that conversion since you have a lot of these videos, but we've only just written that into our next grant and don't if that'll be funded or when. I have a proof of concept python script that really only works with google slides currently.)
Would this be an option for y'all? Because we'd really love to have this tutorial in for everyone to access, and this one requirement would help this resource meet our accessibility commitments.
Tagging in @burkemlou @mcharleston for comments.
My thoughts on videos and accessibility: This tutorial is designed to work without the videos, we've included them as something extra for self-guided learners to be able to access a taste of the in-person workshop experience.
Do you have a tutorial on making GTN formatted slides?
Hi @hexylena,
Thanks for your feedback, it's really useful as always.
Echoing Adam's comments, these videos were created in the spirit of those done for the Smorgasbord events and to do exactly what you're suggesting - provide flexibility in the way that people can interact with the tutorial.
The ideas you suggested for improving accessibility sound good to me. We're always happy to work with you on this!
That said, we're all on leave for at least couple of weeks over Christmas/New Year. I'll get in touch once I'm back in the office (after the 11th January) and we can figure out the best way forward. In the meantime, if you have tutorials or guidelines you can point us towards that would be really helpful.
Thanks again and wishing you a restful end to 2023 and a happy 2024.
Melissa
tagging @Adamtaranto and @mcharleston
I forgot to add, thanks for approving the Zenodo record! We'll add that in next year too.
something extra for self-guided learners to be able to access a taste of the in-person workshop experience
yes, and we love this! that's so great to offer that! from our side, I just want to make sure everyone can access that resource because I think there's a lot of good information in those talks, that might not be available otherwise, and in any case it'll make excellent review materials for a motivated and dedicated learner.
Do you have a tutorial on making GTN formatted slides?
We have some materials, maybe it's time we improved them. There's a slide deck on how to format the slides since they use slightly different markup, but there's no specific tutorial.
The header metadata for a slide deck is essentially the same as a tutorial. I'll work on getting that documented in a better way, we have such a nice tutorial for contributing tutorials, but not for slides yet.
Since y'all're still on break, hopefully I can get some materials together in the meantime!
Hi @hexylena, happy new year!
Any chance we could have a quick chat about this next week?
I'm free Wednesday or Thursday morning before 11am Europe time.
Yes, that's definitely possible. Let's try for wednesday? Could you send a calendar invite? :) 9-10 CET should be doable.
Great, thanks. I've just sent an invite and a Zoom link to your Gmail account.
Talk to you tomorrow.
On Mon, 15 Jan 2024 at 19:39, Helena @.***> wrote:
Yes, that's definitely possible. Let's try for wednesday? Could you send a calendar invite? :) 9-10 CET should be doable.
— Reply to this email directly, view it on GitHub https://github.com/galaxyproject/training-material/pull/4611#issuecomment-1891703829, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQNUHBFLUBEVB23XGMBFI4TYOT2M3AVCNFSM6AAAAABA7DHBPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJRG4YDGOBSHE . You are receiving this because you were mentioned.Message ID: @.***>
From the chat with @burkemlou it's all looking quite positive!
I learned the slides were in beamer format, this is fantastic news, you can then use pandoc to convert them probably pretty easily. I suspect the command will be something like pandoc -f beamer -t reveal.js < slides.tex > slides.html (which will then need some reformatting but I will test that and make a further reply here.)
The biocommons logo can be added to each slide deck, please set the logo field in the metadata header with a path (in-repository) to the image
Since there are fiveish slide decks I would recommend the following: creating a folder for each, with a single slides.html inside.
As I find time I'll start working on a nice widget to embed these and give end-users a choice of their content format, just leave the youtube links as-is until then :)
Edit, I stand corrected about the pandoc conversion, pandoc can only output beamer, it can't use it as input, it can't use any of the slide formats as input sadly.
Looking around, others had similar issues https://rmarkdown.rstudio.com/articles_beamer.html https://stackoverflow.com/questions/39453252/pandoc-to-move-knitr-beamer-slides-to-rmarkdown
So maybe something to try there is just treating it as a plain latex file
12:48:49 w-galaxy:[~/arbeit/galaxy/training-material @pr-4630‽]$ pandoc -f latex -t markdown < /rw/home/user/arbeit/presentations/2019-GCC/gxadmin.tex
# About
::: frame
{width="90%"} \
::: center
Community \| Users \| Training \| Infrastructure
:::
:::
::: frame
About Me
- Joined team 16 months ago
- UseGalaxy.eu System Administrator
- de.NBI Cloud Freiburg Administrator\
(3.5k cores, 15TB ram)
- Developed Galaxy Circos/JBrowse tools, RStudio GIE
:::
# Community
::: frame
Community
::: center
Community is the most important part of what we do
:::
:::
This is, maybe not sooo painful to convert further, then you'd just need to replace all ::: frame with --- to mark the slide transition, and delete the corresponding :::, and it'd be done?
Hi Helene, thanks so much for your kind and useful comments! I was also hoping pandoc would do it but that's ok, I will see how much of a faff it is to convert from my LaTeX to the markdown. :)
Hi @hexylena, do you know why the CI checks are failing on the latest commit?
Also, should I squash the history down into a single commit before it gets merged?
@mcharleston hope pandoc gets you close at least :)
@Adamtaranto I will comment directly on the page for the linting errors but they're easy fixes :)
Also, should I squash the history down into a single commit before it gets merged?
no, please don't do that (or rather, there is no reason from our side to. it's nice to have the history.)
Thanks Helena. I'll start working through your suggestions and get back to you.
Hi @hexylena we're looking into the process of converting slides to markdown and it's looking like it will be a manual process. Being able to preview the slides (like you can for the tutorial itself) as we rebuild them would be very helpful in this process.
Is there a way to do this within GitPod?
Thanks!
Hey @burkemlou, yes, absolutely that can be done in GitPod! It should be done automatically, and it sounds like you're doing that already for the tutorials, could you share what issues are you encountering with the slides?
Thanks @hexylena the issue (at the moment at least) is that we didn't know it was possible. Let us try it out and we'll get back to you if we need more help.
Hi @hexylena I've replaced formulas that were images with math markup which is working great. But I have the peculiar problem that the formulas show up in the preview of the details box. I'm sure I'm missing some tag somewhere but I can't figure it out. Any suggestions?
It's at ~ line 624 in the tutorial.md file
Hi @hexylena I've replaced formulas that were images with math markup which is working great. But I have the peculiar problem that the formulas show up in the preview of the details box. I'm sure I'm missing some tag somewhere but I can't figure it out. Any suggestions?
It's at ~ line 624 in the tutorial.md file
I have fixed this so that the formulas are now contained within the details box. It was something to do with line breaks. I'd like to centre align them but can't get it to work. Left aligned will do!
Hi @hexylena,
Quick update from our side. I think we have now worked through and addressed your comments above. Please let us know if we've missed something.
We have figured out how to convert Michael's slides into the GTN format and have added the first one into the GTN to practice on. We're working on formatting of this slide correctly and converting the remaining slides over.
Michael would like to use this tutorial in teaching from mid-April. If we're able to convert slides over by the end of March do you think we could have it published before then?
Thanks again for your input and help troubleshooting.
Melissa
Tagging @PatCapon39 and @mcharleston for comments on the slide conversion process.
Michael would like to use this tutorial in teaching from mid-April. If we're able to convert slides over by the end of March do you think we could have it published before then?
yes absolutely!
Thank you all for your hard work on this, I cannot wait to announce it in our channels.
@burkemlou since y'all're committed to including the slides, I'd also be open to merging this sooner. Since the tutorial itself looks ready, we could ship that now as is, and as the slides come in we'll update it accordingly to also link to the alternative versions of that.
Would you like to also write a short news post announcing the new tutorial? á la something like https://training.galaxyproject.org/training-material/news/2023/01/26/pathogen-detection-tutorial.html
There are some error messages but I wanted to re-write them here where they're easier to read :)
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[ ] Could you please add a license and creator information to the workflow? (Helps us ensure it's FAIR)
-
[x] youtube linting error is now ignored
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[x] tool IDs have been corrected
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[x] I've added a stub workflow test for the workflow included (no need to do anything)
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[x] I've added a workflow which matches the tutorial more exactly for reproducibility/testing initiatives.
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[x] I've replaced some of the tool execution descriptions with more GTN standard formatting (hierarchies, icons, consistency). Y'all had a few parameters that were defaults, or seemed to be working around odd server issues, I'm not sure what happened there but I found
". Under the Modelling Parameters, click Automatic model selection_ and then under Use Custom Model select "(none))" in the drop-down menu, and click the Automatic model selection menu title again to close it."
to be a very confusing instruction since that seems to be more or less leaving it as default.
there is a 'url failing error' which is because the gtn doesn't support slides not named slides.html, I will think of how to best handle this.
@hexylena I'm having some trouble getting GTN to recognise math markdown using the $$ formatting described here https://training.galaxyproject.org/training-material/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html#writing-mathematical-expressions
The particular file I'm trying to get math markdown to show up on is here https://github.com/Adamtaranto/training-material/blob/dev/topics/evolution/tutorials/abc_intro_phylo/03-msa_GTNformat.html
Any suggestions would be greatly appreciated!
Hi @hexylena,
Thanks for the fixes above.
- Re the workflows, where do we add the licence and creator? I'm having trouble finding corresponding comments.
- Re slide naming. Would renaming to Slides_1.html etc fix this error? We're not wedded to the file names.
And an update on slides in general. We've decided to push ahead and upload all the slides before going live. Michael's teaching schedule has changed which gives us some flexibility with our timeline for getting this done. We are still aiming for ~ end of April.
I'll write a story for the GTN and the BioCommons newsletter once it is out.
having some trouble getting GTN to recognise math markdown using the $$ formatting described here.
@PatCapon39 the most likely cause is that recently i made mathjax load conditionally when it found $$ on the page, to save bandwidth for users. it's likely there is something wrong on my end with that. I'll look into it!
workflows, where do we add the licence and creator?
huh we don't have an faq for this, we really should. If you load the workflow in the galaxy workflow editor you'll find this menu where you can add relevant creators and organisations:
Would renaming to Slides_1.html etc fix this error?
they need to be in separate folders, with a slides.html per folder (at the same level as other tutorials). I can push a commit with this change today probably and provide the linking
We are still aiming for ~ end of April.
that sounds great! I will ensure it is merged by then
Fyi, when testing this tutorial I found some issues with the visualisations, just in case y'all hadn't experienced the same https://github.com/galaxyproject/galaxy/issues/17770
I've split the slide decks into 4 different folders, so they'll pass rendering checks.
And for the math rendering it looks like there is indeed a bug of some sort :( I will look into it further.
in the MSA slide deck I see: internal image images/DPcell.pdf does not exist, is that file maybe missing?