[JOSS Review]: Is "Brief Introduction to PeriDEM Model" section necessary?

[matthewfeickert]

Following openjournals/joss-reviews#7525 (comment), I've read the current state of the paper draft in docs/joss/paper.md on the joss branch. I think things are good, though I'm not certain that the section "Brief Introduction to PeriDEM Model" is needed, given that this is explaining the physics model itself and the JOSS docs note

Your paper should include:

• A list of the authors of the software and their affiliations, using the correct format (see the example below).
• A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
• A Statement of need section that clearly illustrates the research purpose of the software and places it in the context of related work.
• A list of key references, including to other software addressing related needs. Note that the references should include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.
• Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it.
• Acknowledgement of any financial support.

and this section feels both more technical and isn't listed as a requirement.

My personal thoughts are that this section should be moved to the documentation. As far as I can tell this level of detail about the physics model doesn't exist in the docs yet and it only present in doi.org/10.1016/j.jmps.2021.104376.

I also don't think we're even able to use Figure 2 in the paper

PeriDEM/docs/joss/paper.md

Line 64 in 5d3d2f9

{width=40%}

without permission from Elsevier, as those are images used in Figure 2 of doi.org/10.1016/j.jmps.2021.104376 and so Elsevier now owns the copyright to them (unless you self published them in a Zenodo archive or something before publication under a cc license and then cited the archive when using them). Note that I would be very happy to be wrong here. This is a conversation I've had with @kyleniemeyer a few times, and he might have a more informed view on it than I do.

What are you general thoughts on the "Brief Introduction to PeriDEM Model" section? You wrote it and so I don't want to be dismissive of that information, and I think it is nice to have associated with the software, just maybe not in the JOSS paper.

[prashjha]

Hi @matthewfeickert, I would prefer to keep the 'Brief Introduction to PeriDEM Model' in the JOSS paper, and I also liked the idea of including such descriptions in the library documentation. The attached figure differs slightly from the one in the paper. I have used this figure in many of my conferences. I don't see any copyright issues with this figure.

[matthewfeickert]

I would prefer to keep the 'Brief Introduction to PeriDEM Model' in the JOSS paper, and I also liked the idea of including such descriptions in the library documentation.

Okay, that section can stay but I don't think that

The attached figure differs slightly from the one in the paper.

matters in terms of copyright.

I have used this figure in many of my conferences. I don't see any copyright issues with this figure.

When you published https://doi.org/10.1016/j.jmps.2021.104376 you gave full copyright of the contents and any derived work to Elsevier, as the publication is not open access. The Elsevier Permissions page (https://www.elsevier.com/about/policies-and-standards/copyright/permissions) includes publication of published images explicitly in this

As a general rule, permission should be sought from the rights holder to reproduce any substantial part of a copyrighted work. This includes any text, illustrations, charts, tables, photographs, or other material from previously published sources. Obtaining permission to re-use content published by Elsevier is simple. Follow the guide below for a quick and easy route to permission.

Permission is required for any material that is not original. As a rule, written permission must be obtained from the rightsholder to re-use any copyrighted material. Typically, the rightsholder of published material is the publisher unless it is explicitly indicated otherwise. Copyrighted material can include figures, illustrations, charts, tables, photographs, and text excerpts. Re-use of any borrowed material must be properly acknowledged, even if it is determined that written permission is not necessary.

As is, the JOSS draft reuses elements from or makes small edits to the published Elsevier work for

JOSS Draft Figure	https://doi.org/10.1016/j.jmps.2021.104376 Figure
2	2
3a	22
3b	24

(Also, while https://doi.org/10.1016/j.jmps.2021.104376 is cited in the JOSS draft, the figure text makes no reference to the publication.)

Other members of the JOSS editorial team agree that without explicit permissions from the publisher these figures can not be published under JOSS. Though as we're of a difference of opinion on this I would fully encourage you to also check with the EiC team. As we're very close to publishing this JOSS submission it would be great if this could get resolved this week so that the submission can be published before next week.

edit: I see now that you did publish a preprint on arXiv (https://arxiv.org/abs/2010.07218) 👍 , but it uses the arXiv.org perpetual, non-exclusive license 1.0, which is not a CC BY-SA license.

[prashjha]

Hi @matthewfeickert, I contacted Elsevier (see some more details in the Slack channel), and since I am the author of the original article, I retain the rights to reuse and adapt my work as done in this article. They did ask me to acknowledge the published article properly. I already acknowledged the article, but just to be safe, I updated the figure captions to include a reference. I hope this helps address the issue. Once you let me know, I will close it. Thank you for being very diligent about this!

[matthewfeickert]

Resolved by 20fe4b3.

Thanks for all the work you did here in short order, @prashjha. You went above and beyond also sharing everything you learned with the rest of the editorial team, which is going to be quite useful in the future I think. 👍