[REVIEW]: BioPandas: Working with molecular structures in pandas DataFrames

[whedon]

Submitting author: @rasbt (Sebastian Raschka)
Repository: https://github.com/rasbt/biopandas
Version: v0.2.2
Editor: @pjotrp
Reviewer: @krother
Archive: 10.5281/zenodo.804030

Status

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Reviewers and authors:

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Reviewer questions

Conflict of interest

• 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).

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v2.1.0)?
• Authorship: Has the submitting author (@rasbt) made major contributions to the software?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: Have any performance claims of the software been confirmed?

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g. API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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. @krother it looks like you're currently assigned as the reviewer for this paper 🎉.

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[krother]

The PDB parsing works out of the box and does not require further explanation. It is a killer app in itself. I found a (probably small) issue in the RMSD calculation feature.
At this moment, I am unable to establish the functional claims "reading and parsing millions of small molecule structures (from multi-MOL2 files)" and "filtering molecules by the presence of functional groups" based on the documentation.

[krother]

DOI references for the PDB could be:
Nature Structural Biology 10, 980 (2003); doi: 10.1038/nsb1203-980
and
The Protein Data Bank
Helen M. Berman
John Westbrook
Zukang Feng
Gary Gilliland
T. N. Bhat
Helge Weissig
Ilya N. Shindyalov
Philip E. Bourne
Nucleic Acids Res (2000) 28 (1): 235-242.
DOI: https://doi.org/10.1093/nar/28.1.235

[krother]

For pandas, a book written by Wes exists (http://shop.oreilly.com/product/0636920023784.do), but it has no DOI. I'd leave the pandas and MOL reference as they are.

[rasbt]

Thanks for the feedback!

The PDB parsing works out of the box and does not require further explanation. It is a killer app in itself. I found a (probably small) issue in the RMSD calculation feature.

I saw a note about that issue in the biopandas repo and will take a look at it tonight and hopefully resolve it.

At this moment, I am unable to establish the functional claims "reading and parsing millions of small molecule structures (from multi-MOL2 files)" and "filtering molecules by the presence of functional groups" based on the documentation.

When I wrote this I had another paper in mind that I was working on recently. I am just waiting for the co-author feedback and then the manuscript is going to be submitted to JCIM ~ next week. But I guess it will probably take a bit longer until that's published and citable. There, I used biopandas as an engine to perform filtering by functional groups (spatial distance between functional groups, charge range, and hybridization). I only have a brief section on that in the docs here:

http://rasbt.github.io/biopandas/tutorials/Working_with_MOL2_Structures_in_DataFrames/#parsing-multi-mol2-files

In this example, you can think of the # do some analysis placeholder as data frame operations like: does this molecule have a O.2 hybridized and S.o2 hybridized atom? If yes, are those within a distance of X A ... and so forth using and chaining in-built pandas/biopandas functions. I am happy to extend this section with a simple case if necessary. Would that be okay with you? I probably won't do the "million" there because processing millions of molecules could take a few hours (it's a short time for a research project, but maybe a bit to involved for a tutorial :P)

[rasbt]

DOI references for the PDB could be: ...

Thanks, updated those references!

[krother]

argh, I didn't spot the menu bar on top on the documentation page. It's quite impressive and complete as it is, thanks! 👍

[rasbt]

I found a (probably small) issue in the RMSD calculation feature.

This should be fixed in the master branch now (BioPandas/biopandas#34). For JOSS, I assume I need to make a new version release so that this change takes effect? It's not a problem, I think I should hold off a bit though, in case there's something else that needs to be addressed. (Once everything looks fine, I can make a new stable release, i.e., 2.1.0 -> 2.1.1 or 2.2.0). Is that okay?

[krother]

Checked the changed version by installing with pip directly from github. Great you put this in the documentation! And it works, too.

[krother]

Created a PR where I indicated a possible location for the DOI in the PDB reference. No more issues from me. Congratulations to this contribution, it is time to get the word out!

[rasbt]

Thanks @krother . Just merged the DOI PR, and I am happy to hear that everything looks fine now :)

[krother]

OK, review done.

[pjotrp]

@krother thanks! @arfon must be a record here. Ready to R&R.

[arfon]

@rasbt - Could you move the references you currently have in the paper.md file into a paper.bib file and cite them directly please? (You can read how to do that here)

When you've done that could you make an archive 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.

[rasbt]

@arfon no problem.

I moved the references to a separate bibtex file, paper.bib.

When you've done that could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive?

Here's the link for the 0.2.1 version that was reviewed:

https://zenodo.org/record/574879

This existed prior to the submission though and thus, it doesn't include the paper.md and paper.bib files.

I made a new biopandas version (v0.2.1 -> v0.2.2) for zenodo incorporating the paper files and also including a small fix that came up during the review process. The zenodo link and doi:

https://zenodo.org/record/804030

[arfon]

@whedon set 10.5281/zenodo.804030 as archive

[whedon]

OK. 10.5281/zenodo.804030 is the archive.

[arfon]

@krother many thanks for your rapid review here and to @pjotrp for editing this submission ✨

@rasbt - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00279 ⚡️:rocket: :boom:

[rasbt]

That's awesome! Thanks a lot, everyone, for all the work and the very seamless process!