[PRE REVIEW]: BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET #6342

editorialbot · 2024-02-09T18:47:44Z

Submitting author: @PioBeat (Dominik Grzelak)
Repository: https://github.com/bigraph-toolkit-suite/bigraphs.grgen-bigraphs
Branch with paper.md (empty if default branch):
Version: v1.0
Editor: @vissarion
Reviewers: @abhishektiwari, @Ethan-CS, @idoby
Managing EiC: Daniel S. Katz

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/a4588689144a60762ef9a6df20096b2c/status.svg)](https://joss.theoj.org/papers/a4588689144a60762ef9a6df20096b2c)

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editorialbot · 2024-02-09T18:47:46Z

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 · 2024-02-09T18:47:47Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (771.3 files/s, 76903.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            25            385            431           2045
Markdown                         2            177              0            489
TeX                              1             14              0            331
Maven                            1             10             17            294
XMI                             12              0              0            287
XML                              4              0              0            274
YAML                             1              1              4             18
JSON                             2              0              0              9
-------------------------------------------------------------------------------
SUM:                            48            587            452           3747
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-09T18:47:49Z

Wordcount for paper.md is 1992

editorialbot · 2024-02-09T18:48:30Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-030-43916-3 is OK
- 10.1007/978-3-319-75396-6_5 is OK
- 10.1007/978-3-540-31847-7_20 is OK
- 10.1142/9789812562494_0038 is OK
- 10.1007/3-540-31188-2 is OK
- 10.1007/978-3-030-51372-6_3 is OK
- 10.1016/j.dam.2018.07.006 is OK
- 10.1109/VLHCC.2005.23 is OK
- 10.5445/IR/1000007369 is OK
- 10.4204/EPTCS.231.2 is OK
- 10.1016/j.entcs.2007.04.013 is OK
- 10.1007/s00165-011-0184-5 is OK
- 10.1007/978-3-319-41540-6_27 is OK
- 10.1007/978-3-540-89020-1_38 is OK

MISSING DOIs

- 10.1007/3-540-44618-4_19 may be a valid DOI for title: Deriving Bisimulation Congruences for Reactive Systems
- 10.1007/11841883_27 may be a valid DOI for title: GrGen: A Fast SPO-Based Graph Rewriting Tool
- 10.1007/978-3-642-03741-2_28 may be a valid DOI for title: DBtk: A Toolkit for Directed Bigraphs

INVALID DOIs

- None

editorialbot · 2024-02-09T18:49:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-02-09T18:49:55Z

Five most similar historical JOSS papers:

GBOML: Graph-Based Optimization Modeling Language
Submitting author: @MiftariB
Handling editor: @fraukewiese (Active)
Reviewers: @odow, @leonardgoeke
Similarity score: 0.8022

Graph Transliterator: A graph-based transliteration tool
Submitting author: @seanpue
Handling editor: @gkthiruvathukal (Active)
Reviewers: @rlskoeser, @vc1492a
Similarity score: 0.7986

A flexible search system for high-accuracy identification of biological entities and molecules
Submitting author: @maxkfranz
Handling editor: @galessiorob (Active)
Reviewers: @AlexanderPico, @rabdill, @apcamargo
Similarity score: 0.7964

3dfier: automatic reconstruction of 3D city models
Submitting author: @hugoledoux
Handling editor: @arfon (Active)
Reviewers: @GANys, @chenkianwee
Similarity score: 0.7941

BigX: A geographical dataset visualisation tool
Submitting author: @geekysquirrel
Handling editor: @hugoledoux (Active)
Reviewers: @liberostelios, @jvdkwast
Similarity score: 0.7939

⚠️ 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.

danielskatz · 2024-02-09T18:52:37Z

👋 @PioBeat - thanks for your submission. Before we get started with the review, there are a couple of issues:

Your paper is too long. JOSS has a normal upper limit of roughly 1000 words, and your paper is close to 2000. Please see the example paper for an example of a typical JOSS paper. You can use the command @editorialbot check repository to run checks on the repository that include the word count of the paper.
In addition, please work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again.

Once you have made changes in the paper, whether this is content or references, please use the command @editorialbot generate pdf to make a new PDF.

editorialbot commands need to be the first entry in a new comment.

I'll put this on pause until you tell me it's ready to start because these two issues have been resolved.

Finally, regarding the other planned submission, since that hasn't yet happen, it doesn't matter to JOSS. But when you do submit that other paper, be sure to either mention or cite this paper, depending on its status, as I don't know the other journal's policy.

PioBeat · 2024-02-12T09:29:15Z

@editorialbot check references

editorialbot · 2024-02-12T09:29:33Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-030-43916-3 is OK
- 10.1007/978-3-319-75396-6_5 is OK
- 10.1007/3-540-44618-4_19 is OK
- 10.1007/978-3-540-31847-7_20 is OK
- 10.1142/9789812562494_0038 is OK
- 10.1007/3-540-31188-2 is OK
- 10.1007/978-3-030-51372-6_3 is OK
- 10.1016/j.dam.2018.07.006 is OK
- 10.1007/11841883_27 is OK
- 10.1109/VLHCC.2005.23 is OK
- 10.5445/IR/1000007369 is OK
- 10.4204/EPTCS.231.2 is OK
- 10.1007/978-3-662-45917-1_2 is OK
- 10.1016/j.entcs.2007.04.013 is OK
- 10.1007/s00165-011-0184-5 is OK
- 10.1007/978-3-642-03741-2_28 is OK
- 10.1007/978-3-319-41540-6_27 is OK
- 10.1007/978-3-540-89020-1_38 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-12T09:30:28Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-030-43916-3 is OK
- 10.1007/978-3-319-75396-6_5 is OK
- 10.1007/3-540-44618-4_19 is OK
- 10.1007/978-3-540-31847-7_20 is OK
- 10.1142/9789812562494_0038 is OK
- 10.1007/3-540-31188-2 is OK
- 10.1007/978-3-030-51372-6_3 is OK
- 10.1016/j.dam.2018.07.006 is OK
- 10.1007/11841883_27 is OK
- 10.1109/VLHCC.2005.23 is OK
- 10.5445/IR/1000007369 is OK
- 10.4204/EPTCS.231.2 is OK
- 10.1007/978-3-662-45917-1_2 is OK
- 10.1016/j.entcs.2007.04.013 is OK
- 10.1007/s00165-011-0184-5 is OK
- 10.1007/978-3-642-03741-2_28 is OK
- 10.1007/978-3-319-41540-6_27 is OK
- 10.1007/978-3-540-89020-1_38 is OK

MISSING DOIs

- None

INVALID DOIs

- None

PioBeat · 2024-02-12T09:30:39Z

@editorialbot check repository

editorialbot · 2024-02-12T09:30:41Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (894.5 files/s, 88515.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            25            385            431           2045
Markdown                         2            164              0            462
TeX                              1             14              0            335
Maven                            1             10             17            294
XMI                             12              0              0            287
XML                              4              0              0            274
YAML                             1              1              4             18
JSON                             2              0              0              9
-------------------------------------------------------------------------------
SUM:                            48            574            452           3724
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-12T09:30:43Z

Wordcount for paper.md is 1079

PioBeat · 2024-02-12T09:31:35Z

@editorialbot generate pdf

editorialbot · 2024-02-12T09:33:05Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-02-12T09:33:49Z

Five most similar historical JOSS papers:

A flexible search system for high-accuracy identification of biological entities and molecules
Submitting author: @maxkfranz
Handling editor: @galessiorob (Active)
Reviewers: @AlexanderPico, @rabdill, @apcamargo
Similarity score: 0.7963

GBOML: Graph-Based Optimization Modeling Language
Submitting author: @MiftariB
Handling editor: @fraukewiese (Active)
Reviewers: @odow, @leonardgoeke
Similarity score: 0.7956

3dfier: automatic reconstruction of 3D city models
Submitting author: @hugoledoux
Handling editor: @arfon (Active)
Reviewers: @GANys, @chenkianwee
Similarity score: 0.7933

Graph Transliterator: A graph-based transliteration tool
Submitting author: @seanpue
Handling editor: @gkthiruvathukal (Active)
Reviewers: @rlskoeser, @vc1492a
Similarity score: 0.7912

BigX: A geographical dataset visualisation tool
Submitting author: @geekysquirrel
Handling editor: @hugoledoux (Active)
Reviewers: @liberostelios, @jvdkwast
Similarity score: 0.7909

⚠️ 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.

PioBeat · 2024-02-12T10:32:19Z

@danielskatz it's ready to start. The issues should be resolved.

danielskatz · 2024-02-12T13:27:15Z

👋 @Nikoleta-v3 - do you think you would be able to edit this submission?

danielskatz · 2024-02-12T13:27:26Z

@editorialbot invite @Nikoleta-v3 as editor

editorialbot · 2024-02-12T13:27:28Z

Invitation to edit this submission sent!

danielskatz · 2024-02-17T13:06:15Z

👋 @Nikoleta-v3 - pinging again - do you think you would be able to edit this submission?

Nikoleta-v3 · 2024-02-17T17:01:54Z

Hello @danielskatz! My apologies for the delay. The last time I used Java was 8 years ago, so I'm not sure if I will be able to do justice to the submission 😅

danielskatz · 2024-02-17T17:05:41Z

👋 @AoifeHughes - Would you be able to edit this?

danielskatz · 2024-02-17T17:05:50Z

@editorialbot invite @AoifeHughes as editor

vissarion · 2024-03-04T07:22:17Z

Hi, @danielskatz, thanks for the invitation but my Java experience is very limited, so maybe there is a chance for a more suitable editor.

danielskatz · 2024-03-06T10:01:16Z

@vissarion - I wonder if this would be a place where you could depend on the reviewers, even without having so much Java experience?

vissarion · 2024-03-06T10:30:32Z

@danielskatz OK I can do that.

vissarion · 2024-03-06T10:30:43Z

@editorialbot assign me as editor

editorialbot · 2024-03-06T10:30:47Z

Assigned! @vissarion is now the editor

vissarion · 2024-03-06T10:38:28Z

👋 @maxkfranz, @MiftariB, @hugoledoux, @seanpue, @geekysquirrel, it seems that you are all interested in graph problems and algorithms, would any of you be willing to review this submission for JOSS?

MiftariB · 2024-03-06T11:28:08Z

Thanks for the invitation. I will have to turn it down as my Java knowledge is too limited to properly review this article unfortunately.

hugoledoux · 2024-03-07T07:35:17Z

Same here, I'm afraid my Java knowledge is very very low, and I wouldn't be comfortable reviewing this.

vissarion · 2024-03-08T09:49:30Z

Hi @PioBeat do have any reviewers to recommend?

maxkfranz · 2024-03-08T15:09:37Z

👋 @maxkfranz, @MiftariB, @hugoledoux, @seanpue, @geekysquirrel, it seems that you are all interested in graph problems and algorithms, would any of you be willing to review this submission for JOSS?

It looks like an interesting tool, but I'll have to decline.

Since this tool is meant to pair with GrGen.NET, a Windows tool, I won't be able to review this. I don't have a Windows computer.

There's also a lot of Java environmental configuration and build setup here, and unfortunately, that would take up much more time than I have available right now. I strongly suggest adding a Dockerfile with verbatim docker run examples in the readme that work with the existing sample files. That would make it much more tractable for the future reviewers.

All the best with the search for reviewers.

PioBeat · 2024-03-08T15:18:51Z

@maxkfranz If that helps you, GrGen.NET can be run under Linux with "monodevelop".
I think I will attempt to provide a Docker image. That would certainly make the review easier.

@vissarion Currently I do not have any reviewer in mind but I will think about that. Thanks for your help.

abhishektiwari · 2024-03-11T02:48:52Z

@vissarion I will be open to review this software paper. Feel free to add me as additional reviewer.

vissarion · 2024-03-11T10:01:07Z

@editorialbot add @abhishektiwari as reviewer

editorialbot · 2024-03-11T10:01:10Z

@abhishektiwari added to the reviewers list!

vissarion · 2024-03-11T10:07:32Z

Hi @Ethan-CS, @bencardoen, @LCB0B, @abhishektiwari, @fAndreuzzi would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

vissarion · 2024-03-14T11:28:10Z

Hi @gabrielspadon, @sonal-raj, @camillescott, @Materials-Informatics-Laboratory, @idoby would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

idoby · 2024-03-15T09:25:19Z

Hi @gabrielspadon, @sonal-raj, @camillescott, @Materials-Informatics-Laboratory, @idoby would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Hi @vissarion. This isn't my forte but I can try to pretend to say something intelligent during the review. Please consider me as a reviewer but I also advise to try to bring in three reviewers if possible since I'm not confident about my ability to provide an insightful review here.

Ethan-CS · 2024-03-15T09:29:12Z

I’m happy to review this, it’s pretty squarely in my wheelhouse! On 11 Mar 2024, at 10:08, Vissarion Fisikopoulos ***@***.***> wrote: Hi @Ethan-CS<https://github.com/Ethan-CS>, @bencardoen<https://github.com/bencardoen>, @LCB0B<https://github.com/LCB0B>, @abhishektiwari<https://github.com/abhishektiwari>, @fAndreuzzi would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html — Reply to this email directly, view it on GitHub<#6342 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARIYWRW2YPFU6OUSNIR2EL3YXV67ZAVCNFSM6AAAAABDB5LVG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBYGA2DCMZYGU>. You are receiving this because you were mentioned.Message ID: ***@***.***>

vissarion · 2024-03-15T09:30:51Z

@editorialbot add @Ethan-CS as reviewer

editorialbot · 2024-03-15T09:30:53Z

@Ethan-CS added to the reviewers list!

vissarion · 2024-03-15T09:31:08Z

@editorialbot add @idoby as reviewer

editorialbot · 2024-03-15T09:31:11Z

@idoby added to the reviewers list!

vissarion · 2024-03-15T09:31:45Z

Thank you all! I am starting the review thread now.

vissarion · 2024-03-15T09:31:53Z

@editorialbot start review

editorialbot · 2024-03-15T09:31:56Z

OK, I've started the review over in #6491.

editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Feb 9, 2024

editorialbot added Java TeX labels Feb 9, 2024

danielskatz added the paused label Feb 9, 2024

danielskatz removed the paused label Feb 12, 2024

editorialbot assigned vissarion Mar 6, 2024

editorialbot assigned abhishektiwari Mar 11, 2024

editorialbot assigned Ethan-CS Mar 15, 2024

editorialbot assigned idoby Mar 15, 2024

editorialbot closed this as completed Mar 15, 2024

[PRE REVIEW]: BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET #6342

[PRE REVIEW]: BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET #6342

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