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galaxyproject / training-material

A collection of Galaxy-related training material
https://training.galaxyproject.org
MIT License
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A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy #3278

Closed anuprulez closed 2 years ago

anuprulez commented 2 years ago

This PR adds a training material for image segmentation prediction using COVID CT scans in a Jupyterlab notebook. The Jupyterlab notebook is integrated into Galaxy Europe as an interactive tool. The standard Jupyterlab has been augmented with many features such as Git integration, Elyra AI, GPU support and runs inside a Docker container. Moreover, remote processing of long-running deep learning training tasks is also possible via running a Galaxy tool that uploads scripts and datasets to Galaxy history and executes scripts on a remote cluster. The entire analysis comes from the paper: https://www.sciencedirect.com/science/article/pii/S2666990021000069

Ground truth and predicted COVID CT scan masks: true_pred_masks

Remote processing: finished_history_remote_ai

3D protein structure (for a shorter SARS-CoV-2 spike protein sequence of length 300)

3D_300_L_protein

A bit of work is still left for this tutorial such as the addition of another use-case of integration with AlphaFold2. Would love to get some comments from @kxk302 and others as well. Thanks!!

Edit on 25.03.22: It is ready to be reviewed.

ping @bgruening

anuprulez commented 2 years ago

This PR is ready to be reviewed. @kxk302 would you have time to review this? Thanks!

kxk302 commented 2 years ago

Hi @anuprulez Yes, will do.

kxk302 commented 2 years ago

Sorry @anuprulez, did not get to review this today. Will review on Monday! Have a great weekend.

anuprulez commented 2 years ago

@kxk302 no worries, have a nice weekend

kxk302 commented 2 years ago

Hi @anuprulez

I am trying to view your tutorial via gitpod (https://training.galaxyproject.org/training-material/topics/contributing/tutorials/gitpod/tutorial.html). If you look at instructions under 'Already have a fork of the GTN?' you will see that your fork must have a main branch (not master) and it must be up-to-date. Could you please rename your master branch to main and make sure its up-to-date, so I can use gitpod to view your tutorial? Thanks!

hexylena commented 2 years ago

It should be possible to switch branches @kxk302 that tutorial is directed at contributors (not reviewers)

hexylena commented 2 years ago

@kxk302 if you check the very bottom left of gitpod you can change branches there to the one this PR is coming from.

image

anuprulez commented 2 years ago

@kxk302 Yes, will do it

anuprulez commented 2 years ago

@kxk302 I have updated the "master" branch in my fork to "main" (https://github.com/anuprulez/training-material) from which this current feature branch was created and this feature branch is also up-to-date with the galaxyproject/training-material:main. I guess this should work :+1:

kxk302 commented 2 years ago

@kxk302 I have updated the "master" branch in my fork to "main" (https://github.com/anuprulez/training-material) from which this current feature branch was created and this feature branch is also up-to-date with the galaxyproject/training-material:main. I guess this should work 👍

Thanks @anuprulez !

kxk302 commented 2 years ago

@anuprulez I went over the tutorial and made some comments.

anuprulez commented 2 years ago

@kxk302 was it possible for you to install the branch? thanks but I am not able to see your review comments here

kxk302 commented 2 years ago

@kxk302 was it possible for you to install the branch? thanks but I am not able to see your review comments here

@anuprulez if you go tutorial.md in Files Changed tab, you should see my embedded comments. Let me know if you have any issues

anuprulez commented 2 years ago

@kxk302 I am not able to see your comments. Here is the link to the file that I am looking at: https://github.com/galaxyproject/training-material/pull/3278/files?file-filters%5B%5D=.md&show-viewed-files=true&w=1

md_file

Also, Show comments filter is checked for this file but I don't see any comment. Do I miss something? Can you provide the line number of one of your comments? Thanks

kxk302 commented 2 years ago

@anuprulez That's strange! Here is a screen grab. I see the comments myself, but there is a 'Pending' next to it. Not sure what it is. Maybe that is causing you not to see the comments? Screen Shot 2022-03-29 at 10 33 47 AM

kxk302 commented 2 years ago

Can you add me as a reviewer? Maybe that fixes the problem.

anuprulez commented 2 years ago

Can you add me as a reviewer? Maybe that fixes the problem.

No, I tried but I could not add you as a reviewer.

anuprulez commented 2 years ago

@kxk302 thanks for reviewing the tutorial. I have added fixes for the review comments. I have added smaller sections for those that were bigger and organised them as more coherent sections. Would be happy to know your further suggestions.

kxk302 commented 2 years ago

@anuprulez the changes look great. Thank you!

anuprulez commented 2 years ago

can this be merged once the build passes? Thanks!

bgruening commented 2 years ago

I'm halfway through ...

anuprulez commented 2 years ago

I'm halfway through ...

Please let me know if you have any further comments to be fixed/added :)

anuprulez commented 2 years ago

Thanks to all @bgruening @hexylena @kxk302