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[PRE REVIEW]: TrackSegNet: a tool for trajectory segmentation into diffusive states using supervised deep learning #5457

Closed editorialbot closed 11 months ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@hkabbech<!--end-author-handle-- (Hélène Kabbech) Repository: https://github.com/hkabbech/TrackSegNet Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @imagejan, @ajasja Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/e15328db72dcaf7ca7068f171005ad49/status.svg)](https://joss.theoj.org/papers/e15328db72dcaf7ca7068f171005ad49)

Author instructions

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

@hkabbech if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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editorialbot commented 1 year ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41598-019-53663-8 is OK
- 10.1038/s41467-021-26320-w is OK
- 10.1039/C4CP03465A is OK
- 10.1109/TMI.1986.4307764 is OK
- 10.7554/eLife.33125 is OK
- 10.1371/journal.pone.0170165 is OK
- 10.1073/pnas.2104624118 is OK
- 10.1109/ISBI52829.2022.9761672 is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None
editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1153.7 files/s, 56281.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          31            110            194           1030
Markdown                         2             57              0            121
TeX                              1             15              0             99
Fish Shell                       1             18             14             68
C Shell                          1             13              7             35
YAML                             1              1              3             20
-------------------------------------------------------------------------------
SUM:                            37            214            218           1373
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1068

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot query scope

editorialbot commented 1 year ago

Submission flagged for editorial review.

Kevin-Mattheus-Moerman commented 1 year ago

@hkabbech thanks for this submission. I am the AEiC for this track and here to help process initial steps. I have just triggered a scope review by the editorial board, to see if this work is deemed in scope. This is normal for submissions that are rather small e.g. in terms of lines of code. Over the coming ~2 weeks we'll review if this work conforms to our substantial scholarly effort criteria .

In the meantime you can start fixing the potentially missing/invalid DOIs pointed out above :point_up: , you can call @editorialbot check references to check them again, and use @editorialbot generate pdf to update the paper.

hkabbech commented 1 year ago

Thank you @Kevin-Mattheus-Moerman.

FYI this is a resubmission. I have added substantial analysis plots to the pipeline.

Regarding the missing DOI, I believe that there is no associated DOI to cite the keras library.

I am looking forward for your final decision.

Kevin-Mattheus-Moerman commented 1 year ago

@hkabbech thanks for the reminder that this is a resubmission. Would you be able to clearly summarise what changes have been made since the previous submission?

For the record, the pre-review link for the initial submission is here: https://github.com/openjournals/joss-reviews/issues/5270.

hkabbech commented 1 year ago

Below is the note to editor when resubmitting:

Notes to editor: Dear editors, TrackSegNet is a command-line tool permitting the segmentation of trajectories into diffusive states (using a deep neural network) and further dynamics analysis for each tracklet state. We believe in the major importance of our software for the understanding of particle dynamics (primarily protein dynamics, but its use can be extended to any type of trajectory dataset). The method was initially developed in our research group and published in 2019 (10.1038/s41598-019-53663-8). TrackSegNet presents major improvements of our method, and permits easy replicability on other trajectory datasets with additional analysis measurements. TrackSegNet was recently applied for the biophysical motion analysis of the androgen receptor in the nuclear environment (manuscript currently under revision at the Nucleic Acids Research journal). This is a resubmission, we have expended the functionality of TrackSegNet by adding major geometrical analysis plots per tracklet state (velocity autocorrelation curves and distributions of displacement and angle), since the initial submission was judged as "not conform to the substantial scholarly effort criteria of JOSS, due to its relatively small size, and narrow functionality". Hopefully, this time, TrackSegNet is conform to the criteria of JOSS and will be able to go through the revision stage. Kind regards, Helene and Ihor

Kevin-Mattheus-Moerman commented 1 year ago

@hkabbech I have just removed the query-scope flag as the scope review concluded this work may be in scope for JOSS. However it does appear "borderline" in terms of what we typically accept (currently), and the reviewers and handling editor may still raise concerns on scope.

hkabbech commented 1 year ago

Thank you @Kevin-Mattheus-Moerman. I would like to get some updates on this, are there reviewers assigned?

Kevin-Mattheus-Moerman commented 1 year ago

@hkabbech I've been looking for a handling editor. I think some might now be available, so I'll invite them now. Thanks for your patience.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @jmschrei as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

jmschrei commented 1 year ago

Unfortunately, I can't take this on right now. Sorry.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @pdebuyl as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 1 year ago

:wave: @pdebuyl

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @pdebuyl as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @pibion as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

pdebuyl commented 1 year ago

Hi @Kevin-Mattheus-Moerman sorry for not responding. I'd be happy to take this after the summer (sorry bis).

pibion commented 1 year ago

Hi @Kevin-Mattheus-Moerman I can take this submission!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot assign @pibion as editor

editorialbot commented 1 year ago

Assigned! @pibion is now the editor

pibion commented 1 year ago

@hkabbech hello! I'm going to start looking for reviewers, but if you have anyone in mind who may be suitable for reviewing this paper that would help immensely!

hkabbech commented 1 year ago

Hi @pibion, Thanks for your time spent on my submission! Sadly, I do not have anyone in mind who could review my work.

arfon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 year ago

Five most similar historical JOSS papers:

MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues Submitting author: @davidnsousa Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @nnadeau, @mwacaan Similarity score: 0.8207

Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning Models Submitting author: @OllyK Handling editor: @osorensen (Active) Reviewers: @jingpengw, @estenhl Similarity score: 0.8184

OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks Submitting author: @Marcdh3 Handling editor: @akeshavan (Retired) Reviewers: @serine, @vc1492a Similarity score: 0.8122

skedm: Empirical Dynamic Modeling Submitting author: @nickc1 Handling editor: @jakevdp (Retired) Reviewers: @johnh2o2 Similarity score: 0.8110

ParticleTracker: a gui based particle tracking software Submitting author: @mikesmithlab Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @alexlib, @nkeim Similarity score: 0.8065

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

arfon commented 1 year ago

@pibion – this list of most similar previous papers ☝️ might be a good source of reviewers for this submission. Suggest starting with the authors of past similar papers first.

hkabbech commented 1 year ago

Hello @pibion and @Kevin-Mattheus-Moerman Can I get some updates on this..? Still no reviewers found? Thanks!

Kevin-Mattheus-Moerman commented 1 year ago

@pibion please continue your search for reviewers here.

Kevin-Mattheus-Moerman commented 1 year ago

@hkabbech Our sincere apologies for the severe delays this submission has encountered. I have also emailed @pibion to ask them to pick this up. If they are no longer available I will pick this up as editor to proceed as soon as possible.

Kevin-Mattheus-Moerman commented 12 months ago

@editorialbot remove @pibion as editor

editorialbot commented 12 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman commented 12 months ago

@editorialbot assign me as editor

editorialbot commented 12 months ago

Assigned! @Kevin-Mattheus-Moerman is now the editor

Kevin-Mattheus-Moerman commented 11 months ago

@hkabbech I am currently trying to find reviewers for this submission. If you would like to suggest any reviewers at this point, that would be hepful. Please mention their GitHub handles, but leave out the @ symbol.

In addition, please consider the below points:

Kevin-Mattheus-Moerman commented 11 months ago

@thorstenwagner @GavinR1 @imagejan @Oxer11 @jkoefinger @ajasja @VincentStimper would you be interested in reviewing a submission entitled TrackSegNet: a tool for trajectory segmentation into diffusive states using supervised deep learning, for Journal of Open Source Software (JOSS)?

JOSS features a streamlined review process which take place here on GitHub. The review will feature the testing/evaluation of the software, and the review of a short paper.

If you are interested in helping, you can let us know by commenting here.

Thanks!

imagejan commented 11 months ago

Thanks for the invitation, @Kevin-Mattheus-Moerman. Yes, please count me in as reviewer.

Kevin-Mattheus-Moerman commented 11 months ago

@editorialbot add @imagejan as reviewer

editorialbot commented 11 months ago

@imagejan added to the reviewers list!

Kevin-Mattheus-Moerman commented 11 months ago

@imagejan that is great thanks. Note this is a so-called "pre-review" issue where we'll assign reviewers. The actual review takes place in a dedicated "review" issue. I'll let you know when we'll get started.

Kevin-Mattheus-Moerman commented 11 months ago

@thorstenwagner @GavinR1 @Oxer11 @jkoefinger @ajasja @VincentStimper would you be interested in reviewing a submission entitled TrackSegNet: a tool for trajectory segmentation into diffusive states using supervised deep learning, for Journal of Open Source Software (JOSS)?

JOSS features a streamlined review process which take place here on GitHub. The review will feature the testing/evaluation of the software, and the review of a short paper.

If you are interested in helping, you can let us know by commenting here.

Thanks!

VincentStimper commented 11 months ago

I think somebody with a background in experimental cell biology or bioinformatics might be better suited than me to review this paper. Ideally, one of the authors of the paper that the method is based on could do it.

hkabbech commented 11 months ago

@Kevin-Mattheus-Moerman, many thanks for the updates!

@hkabbech I am currently trying to find reviewers for this submission. If you would like to suggest any reviewers at this point, that would be hepful. Please mention their GitHub handles, but leave out the @ symbol.

Unfortunately, I'm not sure if I know people who might help review my submission.

In addition, please consider the below points:

* [x]  Please extend your README with a clear paragraph describing the software purpose/functionality.

* [x]  Please add contributing guidelines to your project. You can write a basic section in your README or you could link to a dedicated CONTRIBUTING.md file (see also: https://contributing.md/how-to-build-contributing-md/).

I modified the README accordingly and added a CONTRIBUTING.md file. I also added a Dockerfile and docker-compose.yaml for the creation of a docker container running the code.