[PRE REVIEW]: OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks

[whedon]

Submitting author: @Marcdh3 (Marcus Hill) Repository: https://github.com/quinngroup/ornet-JOSS Version: v0.1 Editor: @akeshavan Reviewers: @serine, @vc1492a

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Thanks for submitting your paper to JOSS @Marcdh3. Currently, there isn't an JOSS editor assigned to your paper.

@Marcdh3 if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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[whedon]

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[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

OK DOIs

- 10.1101/522763 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kthyng]

Hi @marcdh3! Can you look through this list and suggest some appropriate reviewers for your submission? It helps to have about 5 suggestions if possible.

Please fix the citations in your paper; you can find more details here: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

[kthyng]

Hi @akeshavan and welcome onboard! Would you be interested in editing this?

[Marcdh3]

Hi @kthyng! Thank you for the quick response. Here are my reviewer suggestions:

• serine
• sonal-raj
• vc1492a
• camillescott
• nidhog

Also, I will be working on the citations now, and I'll update you once they are fixed.

[Marcdh3]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Marcdh3]

@kthyng I believe we fixed the citations. Please let us know if there is anything else needing to be fixed.

[kthyng]

@whedon add @akeshavan as editor

[kthyng]

(@akeshavan approved by email)

[akeshavan]

:wave: @camillescott and @nidhog: would you be willing to review this paper for JOSS?

[kthyng]

@whedon add @akeshavan as editor

[kthyng]

@arfon is @akeshavan properly in the system? Can't seem to add her as editor here.

[arfon]

@whedon assign @akeshavan as editor

[whedon]

OK, the editor is @akeshavan

[arfon]

@whedon add @akeshavan as editor

@kthyng it's assign not add for the editor. Sorry for any confusion caused.

[kthyng]

@arfon Oh my goodness. Sorry about that! I almost always copy and paste the whedon commands to be sure they're correct but apparently these times I was sure I was correct! :) Thanks for helping.

[arfon]

@arfon Oh my goodness. Sorry about that! I almost always copy and paste the whedon commands to be sure they're correct but apparently these times I was sure I was correct! :) Thanks for helping.

😁no worries!

[akeshavan]

👋 @serine, @sonal-raj, and @vc1492a -- would you be willing to review this paper for JOSS?

[serine]

This looks interesting. I should be able to take a look at it next week, if I can get a hold of raw/example data. Image analysis isn't my field so I wouldn't know where to source the data from.

One super minor thing, but it feels rather weird to call the repository (repo) ornet-JOSS. I'm assuming JOSS suffix in the name referres to the fact that the tool will be submitted to JOSS for review? If this is the case I think it would be much better to drop JOSS from the repo name, while this is still early days for the repo.

Usually repo's name hints / describes what the content of the repo is and I'd say for a lot of the source code the repo name usually is the name of the tool/library. JOSS paper.md is a very small part of the repo.

Just think about establishing a name for your tool and advertising it to other people.

Cheers

[akeshavan]

@whedon assign @serine as reviewer

[whedon]

OK, the reviewer is @serine

[vc1492a]

@akeshavan thanks for reaching out about the opportunity to review this work. I'll be taking a long vacation in about a week's time and will not be returning until close to the end of January. If that's all right with you and the authors, I'm happy to review this work. However I'll be largely unavailable during that time due to travel.

The work is interesting although it's not typically a field I'm involved in, so my contributions for review in regards to it's utility in the field will be very limited. I can however review for code organization, completeness, documentation suitability, etc. In line with @serine, I'd need to get a hold of some example data in order to review this work effectively - ideally more than one sample in which to test.

Hope this helps!

[akeshavan]

Thanks @vc1492a ! It's holiday season, so I understand that we all will be taking time off.

@Marcdh3 could you upload some raw/example data so that the reviewers can take a look?

[akeshavan]

@whedon add @vc1492a as reviewer

[whedon]

OK, @vc1492a is now a reviewer

[Marcdh3]

I've uploaded some videos that we've been using in the "samples" directory. Inside of that directory are three sub-directories labeled "control", "llo", and "mdivi". Each sub-directory contains a video (.mov) and an initial segmentation mask (.vtk). The sub-directories correspond to video data of HeLa cells that were either in the control group, exposed to pre-forming toxin listeri-olysin O (LLO), or exposed to mitochondria division inhibitor-1 (mdivi-1). These videos should do a good job illustrating the morphology changes of mitochondria under different conditions.

[akeshavan]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1983. Feel free to close this issue now!