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[PRE REVIEW]: Tree Explorer (T-REX): Bridging Phylogenetic and Phenotypic Data for Enhanced Analysis and Interpretation #7271

Open editorialbot opened 1 week ago

editorialbot commented 1 week ago

Submitting author: !--author-handle-->@DamianJM<!--end-author-handle-- (Damian John Magill) Repository: https://github.com/DamianJM/T-REX Branch with paper.md (empty if default branch): main Version: v1.2 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/978a162b0484f3cb4f64d5009c560db8/status.svg)](https://joss.theoj.org/papers/978a162b0484f3cb4f64d5009c560db8)

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

@DamianJM if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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editorialbot commented 1 week 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:

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

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editorialbot commented 1 week ago

:warning: An error happened when generating the pdf.

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot set main as branch

editorialbot commented 1 week ago

Done! branch is now main

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot check repository

editorialbot commented 1 week ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (398.4 files/s, 99891.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2            197            208           1017
Markdown                         3             70              0            156
TeX                              1              6              0             77
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                             7            274            212           1269
-------------------------------------------------------------------------------

Commit count by author:

    19  DamianJM
     1  Damian Magill
editorialbot commented 1 week ago

Paper file info:

📄 Wordcount for paper.md is 885

✅ The paper includes a Statement of need section

editorialbot commented 1 week ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week 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 week ago

Five most similar historical JOSS papers:

SuchTree: Fast, thread-safe computations with phylogenetic trees Submitting author: @ryneches Handling editor: @karthik (Retired) Reviewers: @giraola Similarity score: 0.7520

Ngesh: a Python library for synthetic phylogenetic data Submitting author: @tresoldi Handling editor: @majensen (Active) Reviewers: @DavidNickle, @rvosa Similarity score: 0.7344

Phylen: automatic phylogenetic reconstruction using the EggNOG database Submitting author: @giraola Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @juanvillada Similarity score: 0.7285

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens Submitting author: @huddlej Handling editor: @majensen (Active) Reviewers: @dcnickle, @Maghnuso Similarity score: 0.7255

SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. Submitting author: @andrewjpage Handling editor: @biorelated (Retired) Reviewers: @brainstorm Similarity score: 0.7193

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot query scope

editorialbot commented 1 week ago

Submission flagged for editorial review.

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1093/bioinformatics/17.8.754 is OK
- 10.1093/molbev/msw046 is OK
- 10.1038/s41576-020-0233-0 is OK
- 10.1093/nar/gkab301 is OK
- 10.1093/molbev/msu300 is OK
- 10.1093/bioinformatics/btu033 is OK
- 10.1093/molbev/msab120 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
Kevin-Mattheus-Moerman commented 1 week ago

@DamianJM thanks for this resubmission, and for making some changes to address the points we raised. Below is a copy of points raised over at the original submission: https://github.com/openjournals/joss-reviews/issues/7234

The following includes some of the reasons for the rejection and other points on the paper/repository, and should be addressed in full if a future re-submission is of interest:

As you can see I've ticked the boxes that I think are addressed. For the remaining box, on being in scope for JOSS, I've just asked the editorial board for help (by flagging this submission for a scope query). This scope review should take about 2 weeks to complete.

We agree that having a cutoff e.g. at 1000 LOC is arbitrary, and indeed a small number of LOC could be the sign of highly elegant and optimised code that received a lot of thought/attention. And of course, the number of lines of code for a particular problem will vary from one language to another. However, at JOSS we do receive a large number of packages that are very minor in nature, and which could be <3 months of work. Such packages are often "minor utility" or single functionality packages, and are typically not in scope. Furthermore we also receive many "immature" packages (e.g. single contributor quick dump of code, no license, missing testing/documentation etc.). It can be very hard to make these scope calls, but I hope to convince you it is not solely the number of lines of code that we base our decision on. As I said, I've now asked the board for help, so my colleagues, whose expertise is closer aligned with this topic, will help judge if this work should be in scope as well. Thanks.

DamianJM commented 1 week ago

Hi @Kevin-Mattheus-Moerman,

I appreciate this comment and your rapid reconsideration of the manuscript. I can also appreciate the need for strict screening criteria with JOSS as I can imagine it would be easy to be bombarded with numerous submissions. Thank you for passing on the submission for consideration. Work on the project will continue and regardless of the outcome here I hope for some good feedback on possible improvements.

Thanks