[REVIEW]: PyGBe-LSPR: Python and GPU Boundary-integral solver for electrostatics

[whedon]

Submitting author: @ncclementi (Natalia C. Clementi)
Repository: https://github.com/barbagroup/pygbe
Version: 0.3
Editor: @katyhuff
Reviewer: @kyleniemeyer
Archive: 10.5281/zenodo.1067773

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Reviewer questions

@nicoguaro, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @katyhuff know.

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• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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General checks

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• Version: Does the release version given match the GitHub release (0.3)?
• Authorship: Has the submitting author (@ncclementi) made major contributions to the software?

Functionality

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• Functionality: Have the functional claims of the software been confirmed?
• Performance: Have any performance claims of the software been confirmed?

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• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
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• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @nicoguaro it looks like you're currently assigned as the reviewer for this paper 🎉.

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[labarba]

@nicoguaro : Do you have access to a GPU to run this? Let us know if you need anything.

[nicoguaro]

@labarba, I have a GTX 850M in my laptop... but it just stopped working. I will try in a computer in the office that has a G98 Quadro NVS 420.

It seems a little bit more complicated than I thought.

[kyleniemeyer]

@katyhuff I can jump in to review this if needed, as I do have access to a few GPU systems (and reviewed the original PyGBe submission)

[katyhuff]

Thanks a lot @nicoguaro for giving this a look! The particular hardware constraints of this paper may require an editor with access to an appropriate GPU resource. In the future, we may have a journal-wide solution to unique architectural requirements. After some discussion with him here at SciPy, I believe that @kyleniemeyer may be able to conduct the review with the GPU resources he has available to him. @kyleniemeyer , would you be willing to review this paper?

[katyhuff]

@whedon assign @kyleniemeyer as reviewer

[katyhuff]

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[whedon]

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[arfon]

@whedon assign @kyleniemeyer as reviewer

[whedon]

OK, the reviewer is @kyleniemeyer

[katyhuff]

@kyleniemeyer : what's the status on the review of this? Thanks!

[kyleniemeyer]

Regarding the community guidelines, there is a short section in the Developer's Guide docs page (http://barbagroup.github.io/pygbe/docs/contributing.html) that discusses contributing.

This is probably sufficient, but putting a link to this or a "Help" section in the README (since most people will likely enter the project via it on the main repo page) might strengthen this area.

Also, you might consider adding a code of conduct to the project, and mentioning that in both places.

[kyleniemeyer]

The installation instructions are great—the only hiccup I faced was building PyCUDA on one system. You might consider checking for compatibility/updating with the latest version, PyCUDA 2017.1.1.

[kyleniemeyer]

Regarding the article, I have a number of comments and suggestions:

• I think you should add more at the beginning that explains the target problems in more general terms. In particular, each of "biomolecular electrostatics", " nanoparticle plasmonics ", and "boundary integral method" could be briefly explained. Similarly, LSPR isn't really explained—overall, the third paragraph is nearly impossible to understand (for me, at least) due to the heavy use of jargon.

  (I believe our changes to expectations/guidelines for article content and length happened after you originally submitted this.)

• Also, personally I recommend that references not be treated as objects in the text (i.e., rather than "see @Mayergoyz2007", do "see Mayergoyz and Zhang (@Mayergoyz2007)", but I recognize this is a style preference. Just a suggestion 😄

• For the last sentence, I would at minimum change to "We plan to use PyGBe-LSPR to study nanobiosensors and to explore nanophotonics applications." (originally missing period at the end, and "to the study of" -> "to study")

• I see reference @CooperClementiBarba2015 in the .bib file; you might consider adding a mention of that to the paper, if the software was used for that study (but update the reference info). Also, maybe the other papers that are mentioned in the docs?

[kyleniemeyer]

Regarding running the code itself, my main comment is that the Run PyGBe page could include more information about what is output to the screen when running.

Perhaps this is due to me not being familiar with the problems being solved, but explanations of Esolv, Esurf, Ecoul, or Time Cext and Cext per surface would help there.

[kyleniemeyer]

If the above issues can be addressed satisfactorily, and the issues I raised in the repo itself addressed/closed, then I would consider the submission ready to accept.

[ncclementi]

Thanks @kyleniemeyer
We're are working on the suggestions, we'll address them and get back to you here.

[labarba]

Responses to reviewer comments in order of appearance:

Regarding the community guidelines, there is a short section in the Developer's Guide docs page (http://barbagroup.github.io/pygbe/docs/contributing.html) that discusses contributing.

This is probably sufficient, but putting a link to this or a "Help" section in the README (since most people will likely enter the project via it on the main repo page) might strengthen this area.

We added a sentence in the README, with a link to the Developoer's Guide.

Also, you might consider adding a code of conduct to the project, and mentioning that in both places.

We thought about this, and decided that for now, this would be overkill, because we haven't had any contributors from outside the group. We'll revisit this in the future, as needed.

The installation instructions are great—the only hiccup I faced was building PyCUDA on one system. You might consider checking for compatibility/updating with the latest version, PyCUDA 2017.1.1.

We updated the compatibility of dependencies for the latest versions of all our packages, and we added a Docker file to make the installation process easier (in case the user is familiarized with Docker).

I think you should add more at the beginning that explains the target problems in more general terms. In particular, each of "biomolecular electrostatics", " nanoparticle plasmonics ", and "boundary integral method" could be briefly explained. Similarly, LSPR isn't really explained—overall, the third paragraph is nearly impossible to understand (for me, at least) due to the heavy use of jargon.

In the revised first paragraph, we explain "biomolecular electrostatics" by saying what we compute: the solvation energy, and explaining what this is (and what it is used for). We don't explain "boundary integral method," because of the same reason we wouldn't expalin "finite difference method"—it is a standard method in the arsenal of numerical computing. We revised the third paragraph, explaining LSPR, which also helps get an idea of what part of nanoplasmonics we're tackling.

Also, personally I recommend that references not be treated as objects in the text (i.e., rather than "see @mayergoyz2007", do "see Mayergoyz and Zhang (@mayergoyz2007)", but I recognize this is a style preference. Just a suggestion.

We agree completely. But notice that the JOSS machinery produces the correct format when generating the PDF, with Author (YEAR) spelled out, as needed when part of a sentence. In other words, the way we have it in the paper.md file will produce what you want in the final PDF.

For the last sentence, I would at minimum change to "We plan to use PyGBe-LSPR to study nanobiosensors and to explore nanophotonics applications." (originally missing period at the end, and "to the study of" -> "to study")

Fixed.

I see reference @cooperclementibarba2015 in the .bib file; you might consider adding a mention of that to the paper, if the software was used for that study (but update the reference info). Also, maybe the other papers that are mentioned in the docs?

That paper used the previous version of the code, and we added the reference in the first paragraph.

Regarding running the code itself, my main comment is that the Run PyGBe page could include more information about what is output to the screen when running.

Perhaps this is due to me not being familiar with the problems being solved, but explanations of Esolv, Esurf, Ecoul, or Time Cext and Cext per surface would help there.

We modified the printed output so that a short description appears before each instance of the returned variables. Morover, there is a section in the main page of the Documentation (now renamed "Code Documentation:") where a user can search by variable name or keyword, to be pointed to the relevant docstring(s).

[kyleniemeyer]

Thanks @labarba, looks good!

@katyhuff at this point I recommend accepting the submission.

[katyhuff]

Wonderful! Thanks @labarba @ncclementi and @kyleniemeyer !

@labarba and @ncclementi : Could you make an archive of the current version of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[arfon]

@labarba and @ncclementi : Could you make an archive of the current version of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

Friendly reminder on this @ncclementi.

[labarba]

This is me being a bottleneck. We had the problem of the Zenodo archive being created by one student who has now left the group. Zenodo does not have the feature to allow org accounts or sharing the ownership of a Zenodo entry. We exchanged emails with them to have this archive transferred to another account. They said yes, with approval of original uploader. This happened. Now, I have to create a new Zenodo account with a "barbagroup" org email I created, and transfer ownership of the Zenodo entry. Will update here when done.

[ncclementi]

@arfon Here is our zenodo doi: https://doi.org/10.5281/zenodo.1067773

[arfon]

@whedon set 10.5281/zenodo.1067773 as archive

[whedon]

OK. 10.5281/zenodo.1067773 is the archive.

[arfon]

@ncclementi @labarba - when you get a chance, please merge this PR which updates the JOSS paper to the newer format.

[arfon]

@kyleniemeyer many thanks for your review and to @katyhuff for editing this submission ✨

@ncclementi @labarba - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00306 ⚡️ 🚀 💥