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carpentries-incubator / deep-learning-intro

Learn Deep Learning with Python
https://carpentries-incubator.github.io/deep-learning-intro/
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Add JOSE paper #366

Closed svenvanderburg closed 9 months ago

svenvanderburg commented 11 months ago

Fixes #364

Authors

@annefou @florian-huber @dafnevk @psteinb @bpmweel @colinsauze @samumantha @dsmits @CunliangGeng @cpranav93 Do you want to be involved in the JOSE paper on the deep learning lesson? You don't need to do much, it would be nice to get your feedback/contributions when the draft is finished, but it is just a short paper (1000 words max) so we don't necessarily need feedback from everyone.

If you want to be involved, can you check and update your author details in the paper.md file? If you don't respond before 1 September 2023 I assume that you have other priorities at this moment and you will not be on the paper.

Did we miss anyone that did important contributions to the lesson?

Leave your feedback!

UPDATE 8th of August: I just committed the first full draft of the paper and I am looking for feedback, can you review this in this PR? Big feedback is welcome, but since it is a small paper and most of the work is actually in our lesson, it is fine to just leave one or two comments and a thumbs up :)

@colinsauze and @psteinb there is a specific question for you in there, search for @colin and @peter.

UPDATE 1 September

I plan to incorporate your final comments and submit this to JOSE on the 15th of September. If you have time please read through the paper one more time and leave your final comments (just a thumbs up is also fine of course) at the latest the 14th of September

If you need some examples checkout some of the recently published papers here: https://jose.theoj.org/.

Timeline

To do:

github-actions[bot] commented 11 months ago

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/deep-learning-intro/compare/md-outputs..md-outputs-PR-366

The following changes were observed in the rendered markdown documents:

 md5sum.txt     |   1 +
 paper.md (new) | 200 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 201 insertions(+)
What does this mean? If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2023-09-26 11:46:58 +0000

annefou commented 11 months ago

Hi @svenvanderburg my affiliation is correct. I would be happy to help. Please ping me whenever you need me. Many thanks for doing this.

svenvanderburg commented 11 months ago

@tobyhodges I totally forgot you! I think your contributions are superhelpful, do you want to be in the paper? If so, what is your affiliation?

tobyhodges commented 11 months ago

Thanks @svenvanderburg I'd be happy to contribute and be listed as an author. I currently have no official affiliation, while I take a short break from The Carpentries team, but I expect to be back in the role of Director of Curriculum from mid-September 2023. For the purposes of the paper (which I guess will not be submitted until at least next month anyway?) I think it will be fine to list my affiliation as to The Carpentries. I will update you if anything changes unexpectedly.

svenvanderburg commented 11 months ago

@annefou @florian-huber @dafnevk @psteinb @bpmweel @colinsauze @samumantha @dsmits @CunliangGeng @cpranav93 @tobyhodges I just committed the first full draft of the paper and I am looking for feedback, can you review this in this PR? Big feedback is welcome, but since it is a small paper, we are with many and most of the work is actually in our lesson, it is fine to just leave one or two comments and/or a thumbs up :)

colinsauze commented 11 months ago

Authors @annefou @florian-huber @dafnevk @psteinb @bpmweel @colinsauze @samumantha @dsmits @CunliangGeng @cpranav93 Do you want to be involved in the JOSE paper on the deep learning lesson? You don't need to do much, it would be nice to get your feedback/contributions when the draft is finished, but it is just a short paper (1000 words max) so we don't necessarily need feedback from everyone.

My affiliation is correct. I'm not at work next week and tomorrow is already quite busy, but I can take a look at this when I get back on the 21st.

psteinb commented 11 months ago

I totally love the idea of this PR! Thanks @svenvanderburg and others for pushing this lesson ... even to a publication. Kudos!

svenvanderburg commented 11 months ago

Thank you @tobyhodges, @florian-huber, @annefou, @samumantha, @colinsauze, @psteinb for all your super useful comments. I tried to implement all of your comments into the paper. I either committed your suggestions directly, or linked to the commit hash pointing to my changes related to your comment. I hope you like the result!

I plan to incorporate your final comments and submit this to JOSE on the 15th of September. If you have time please read through the paper one more time and leave your final comments (just a thumbs up is also fine of course) at the latest the 14th of September

@CunliangGeng , @bpmweel, @dafnevk if you don't respond by 14th of September, we will not add you as authors to the paper.

colinsauze commented 10 months ago

Thanks for all your work on this @svenvanderburg, it looks really good to me. If it isn't too late, there was just one very minor thing I wanted to fix, Lisana Paladin was also a key contact for running this at EMBL alongside Renato Alves. Before adding her, I just wanted to check if there was some reason she wasn't included in the acknowledgements?

svenvanderburg commented 10 months ago

Thanks for all your work on this @svenvanderburg, it looks really good to me. If it isn't too late, there was just one very minor thing I wanted to fix, Lisana Paladin was also a key contact for running this at EMBL alongside Renato Alves. Before adding her, I just wanted to check if there was some reason she wasn't included in the acknowledgements?

@colinsauze Oh, that's just because I didn't know about Lisana. Of course if Lisana was important for running this at EMBL we should mention that in the acknowledgements! Feel free to add, or if you don't do it I will do it later.

svenvanderburg commented 9 months ago

Merging this as all comments were resolved. We are awaiting https://github.com/carpentries-lab/reviews/issues/25, then we can submit the paper to JOSE.