New tutorial: "Phylogenetics: back to basics"

[Adamtaranto]

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 (michael.charleston@utas.edu.au)
Adam Taranto (adam.taranto@unimelb.edu.au)
Melissa Burke (melissa@biocommons.org.au)

[burkemlou]

Hello @hexylena - following up on your request to update the workflow file from a while back.

I tried loading the tree-bulding.ga file into Galaxy but I get an error 'Uncaught exception in exposed API method:'. I can load other .ga files so it seems to be something about this one. Any suggestions? I haven't used this feature before so let me know if I'm doing something odd here.

Alternatively, I can see in the .ga file that there is this part:

"creator": [
{
"class": "Person",
"identifier": "0000-0001-9760-8992",
"name": "Helena Rasche"
}
],
"format-version": "0.1",
"license": "MIT",

Is this the part that needs updating? I can do that manually and add a CC-BY licence. Is there a particular format needed for the licence?

@Adamtaranto and @mcharleston I see that we still have main_workflow.ga and main_workflow-tests.yml files in the folder for this tutorial. These seem to be copies of the workflow from another tutorial. Do we need these files or are they left over from when you were first setting up the folders and structure for the tutorial?

Nearly done with the slides here. I'll get back to you later in the week.

[hexylena]

@burkemlou I've updated the tree-building.ga that would not load in galaxy, it loads now. I cannot explain the issue, but it seems like the tool was updated and now it works.

I see that we still have main_workflow.ga and main_workflow-tests.yml files in the folder for this tutorial. These seem to be copies of the workflow from another tutorial. Do we need these files or are they left over from when you were first setting up the folders and structure for the tutorial?

ahh that would explain for me why they didn't match at all the tutorial, it was why I ended up making the main-workflow.ga file (7fa178f) based on the instructions of the tutorial (hence the creator information in that file). But please feel free to change its license to whatever you prefer (and make any improvements or changes you like.)

In that case perhaps we can delete them?

[burkemlou]

@hexylena @mcharleston FYI I have a problem with visualising the outputs of IQTREE and FASTREE related to this activity:

`Estimating a Maximum Likelihood tree with IQTree

Find the {% tool IQTree %} program in the tool finder, and run it with the following parameters:

In "General options":
{% icon param-file %} "Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format.": your aligned sequence data (output of MAFFT {% icon tool %})
"Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences": DNA
In "Modelling Parameters":
In "Rate heterogeneity":
"Write maximum likelihood site ratios to .mlrate file": Yes
In "Bootstrap Parameters":
In "Ultrafast bootstrap parameters":
"Specify number of bootstrap replicates (>=1000).": 1000
Click "Run tool".

Click on the output of IQ-Tree and select the visualisation icon. Select 'Phyloviz' to view your tree.`

The visualisation is not working at all in Galaxy AU (Galaxy Australia Support request. 199713). It produces a tree in Galaxy EU but the options to modify the tree are not working as expected (also logged). Galaxy AU reports that this is not trivial to fix.

@mcharleston can we consider a different tool for the purposes of this tutorial?

[hexylena]

Yes I saw the same last month, and filed it as galaxyproject/galaxy#17770 and pinged some folks (@neoformit et al).

I thought I linked it here to ensure everyone was in the loop but seems like I potentially forgot to since I can't find it now.

I don't know what to do about that, perhaps y'all can use an external visualisation (they can maybe copy paste their newick) because galaxy isn't working at all for tree viz.

[burkemlou]

Thanks @hexylena I must have missed that. Glad to know it's not something silly that I'm doing. I'll have a chat with Michael and see if we can come up with an alternative.

[burkemlou]

@hexylena Good news! We have an alternative for Phyloviz!

I've just updated the materials to use Newick Display instead of Phyloviz for visualising the trees from the output of FASTREE and IQTree. I've also added a note that this can be done outside of Galaxy using SplitsTree or FastTree.

With this done, we don't have any more changes to make on our end.

If it's looking okay from the GTN side of things, I think we're ready to publish (hooray!).

Do let me know if you spot something that needs changing though.

[hexylena]

@burkemlou fantastic news! I'll have a look today

[shiltemann]

@burkemlou @Adamtaranto @mcharleston et al. This is awesome! Thanks so much for your contribution and hard work here 🎉

I took the hands-on out of draft mode, I hope that was the intention (if not, let me know and we can put it back in draft mode)

Would you like to create a GTN news item about this? I think it would be very nice to highlight. Here are instructions: https://training.galaxyproject.org/training-material/faqs/gtn/gtn_news_create_post.html, or feel free to simply provides us with some text for the post. We can then also easily post about it on social media etc :)

One thing that would be very cool to add in the future, would be speaker notes for all the slide decks. That not only helps others re-use your materials in their classes/workshops, but the GTN framework will then also create automated lecture videos (using text-to-speech) for you (example).

This can all be done in a follow-up PR and can be done one slide deck at a time, but something to think about :)

[burkemlou]

🎉🎉🎉🎉 Yey!!! Thank you @shiltemann we're very excited that this is out in the world.

And thank you also to you and @hexylena for all your help with formatting, troubleshooting and getting the slides/videos to work.

I'll write a news article for the GTN this week and get that posted ASAP.

Thanks for the suggestion about the speaker notes. There are already videos and transcripts associated with these slides. Perhaps we can use the transcript to make speaker notes in the future. Something to think about as you said.