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datacarpentry / semester-biology

Forkable teaching materials for course on working with data in R
http://datacarpentry.org/semester-biology
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Preparing to submit Data Carpentry Semester Biology to the Journal of Open Source Education #907

Closed ethanwhite closed 2 years ago

ethanwhite commented 3 years ago

Hi everyone - I'm planning to submit this course to the Journal of Open Source Education in the next couple of months. The material is increasingly widely used and I think the folks who have actively contributed in a variety of roles over the years deserve some much earned credit for their contributions to this valued open educational resource.

An initial look through the commit log, issue queue, and my brain suggests that at least the following folks should be included as authors on this publication:

Everyone on this list has contributed significantly in areas including material development, material review & feedback, teaching in the course (and providing active feedback while doing so), producing data for exercises, and big picture planning and design. Please indicate your agreement with being involved in a response below, let me know if you want to review the short summary of the course I need to write for JOSE before I submit, and provide the following information:

 - name: Ethan White
 - affiliation: Department of Wildlife Ecology and Conservation, University of Florida
 - orcid: 0000-0001-6728-7745

I'm happy to chat with anyone who has questions about if they deserve authorship, but I am personally convinced that all of you do.

To anyone not on this list who has made a meaningful contribution to the project please let me know. This effort has been around in one form or another for over a decade and it is easy to lose track of significant contributions that don't show up in the places that are easy to check.

Right now the To Do list for getting things submitted is:

I will ping this issue as things progress. Let me know if you have any questions.

ethanwhite commented 3 years ago

P.S. - I just checked and the course site has now been viewed over 300,000 times!

davharris commented 3 years ago

Thanks Ethan!

Name: David Jay Harris Orcid: 0000-0003-3332-9307 Affiliation: Probably UF? I don’t see a reason to mention Chewy

I’ll waive the option to review the paper before submission, if that’s okay.

Thanks again! Hope you’re all doing well

Dave

On Jan 15, 2021, at 10:58 AM, ethanwhite notifications@github.com wrote:

 P.S. - I just checked and the course site has now been viewed over 300,000 times!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

KristinaRiemer commented 3 years ago

This seems like a great idea! I'd be happy to review anything that you would like feedback on.

MarconiS commented 3 years ago

Thanks @ethanwhite!

Name: Sergio Marconi Orcid: 0000-0002-8096-754X Affiliation: School of Forest Resources & Conservation, University of Florida

Happy to contribute to any point of the ToDo list.

Take care you all!

brymz commented 3 years ago

I'm in!

I can also acknowledge my spin-off of the course platform: Introducing Agroecology

Also, how do you go about tracking those page views? My bosses want to know.

andrewmarx commented 3 years ago
garezana commented 3 years ago

name: Virnaliz Cruz affiliation: School of Natural Resources and Environment, University of Florida orcid: 0000-0001-6783-2651

Echoing what Sergio said.

ethanwhite commented 3 years ago

I've finally finished doing the rest of the manual captioning fixes, which was the big task to do before proceeding. I've gone ahead and released and archived the current version of the course.

The big thing left to do now is write the paper. I've created a stub for the paper on Google Docs: https://docs.google.com/document/d/1-3eXqHs3Q9GOEHg5Hnvu12-kE_nAm1AzYxPipsie6DY/edit?usp=sharing

It currently only contains a title, the author line, and the acknowledgements. I'll try to put together a short outline and then anyone who wants to do some writing is welcome to jump in and help out.

ethanwhite commented 3 years ago

About 6 months later than expected I think we're basically ready to go for submission. If @andrewmarx @brymz @KristinaRiemer @garezana & @skmorgane can all take a look at the ms:

https://docs.google.com/document/d/1-3eXqHs3Q9GOEHg5Hnvu12-kE_nAm1AzYxPipsie6DY/edit

make any edits (in Suggesting mode) that you think are appropriate, and sign-off on submission, then I can start working on (finally) getting this out the door.

ethanwhite commented 3 years ago

@davharris - I'm counting you as having signed off already based on:

I’ll waive the option to review the paper before submission, if that’s okay.

But let me know if that's changed.

brymz commented 3 years ago

Thanks, @ethanwhite. Nice to see it come together! I've got the review on my list for this week or early next.

KristinaRiemer commented 3 years ago

I added some comments and minor edits to the draft.

skmorgane commented 3 years ago

This looks great. I made some minor edits. Looks good to submit to me.

MarconiS commented 3 years ago

looks good to me too. Awesome job!

ethanwhite commented 3 years ago

Thanks everyone!

@KristinaRiemer & @skmorgane - I've integrated your excellent comments and edits.

@KristinaRiemer - Are you happy for this to be submitted now?

Thanks @MarconiS!

@brymz - I've integrated your comments so far. Was that all of them or are you still working on things?

KristinaRiemer commented 3 years ago

@ethanwhite looks great! I definitely sign off on having it be submitted.

brymz commented 3 years ago

@ethanwhite: I just completed my review and approve for submission.

The only idea I had that was not well served in the paper is a comment on the transcendent(?) structure of the course. We state that other instructors can repurpose the course design for other programming courses, but I think we could go further. The modular framework of the course can be agnostic to course customization and content. I used the course structure to develop a site focused on extension programming and structured workshops. No strong feelings here. Just an idea.

Hi, everyone! All the best.

andrewmarx commented 3 years ago

@ethanwhite I've added the last of my comments/edits

ethanwhite commented 3 years ago

Thanks @andrewmarx & @brymz! I've got both of your comments integrated.

@brymz - I think that's a good point about the general infrastructure for the course. I added the following to the end of the "Course Infrastructure" section:

This general infrastructure for modular, collaborative, and accessible course development is useful regardless of the content of the course. For example, one of the authors (Zachary Brym) uses the same infrastructure for teaching a course on agroecology at the University of Florida. We hope that open courses on other topics can be built on this infrastructure to support the broader adoption of collaborative course development for college and university classrooms.

Thanks @KristinaRiemer!

davharris commented 3 years ago

Thanks everyone! I’ll still waive the option to review.

Dave

On Aug 20, 2021, at 1:31 PM, ethanwhite @.***> wrote:

 Thanks @andrewmarx & @brymz! I've got both of your comments integrated.

@brymz - I think that's a good point about the general infrastructure for the course. I added the following to the end of the "Course Infrastructure" section:

This general infrastructure for modular, collaborative, and accessible course development is useful regardless of the content of the course. For example, one of the authors (Zachary Brym) uses the same infrastructure for teaching a course on agroecology at the University of Florida. We hope that open courses on other topics can be built on this infrastructure to support the broader adoption of collaborative course development for college and university classrooms.

Thanks @KristinaRiemer!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

ethanwhite commented 3 years ago

Thanks to everyone for their great contributions to the paper both here and in separate discussions. I've gotten them all integrated and just pushed the submit button.

Screenshot of the submission page for JOSE showing the paper officially submitted

It's been a pleasure working with you on all of this as it has been on the course. I'm going to close this issue and will open new ones to address things to fix during the review process.

ethanwhite commented 2 years ago

Just a quick update that we got very positive reviews at JOSE with only a few small changes requested for publication (fix some broken links, fix a bug that was trying to show solutions on documentation pages, and add some dependency information for local builds). I have done all of that (those of you following the repo will have seen this happening via issues over the last couple of months) and just let the JOSE editor know that these are done (https://github.com/openjournals/jose-reviews/issues/139#issuecomment-1005848404) along with shipping a new release with the changes (https://github.com/datacarpentry/semester-biology/releases/tag/v4.2.0).

Based on previous experiences with JOSS I expect that there may be a couple of small additional changes requested by the editor after some checks and then hopefully we'll be all done.

ethanwhite commented 2 years ago

We are now published at JOSE!!! https://doi.org/10.21105/jose.00139

Thanks again to everyone who has contributed to the course over the years and congratulations!

MarconiS commented 2 years ago

This is awesome! Congrats!