[REVIEW]: BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET #6491

editorialbot · 2024-03-15T09:31:55Z

Submitting author: @PioBeat (Dominik Grzelak)
Repository: https://github.com/bigraph-toolkit-suite/bigraphs.grgen-bigraphs
Branch with paper.md (empty if default branch):
Version: v1.2.0
Editor: @vissarion
Reviewers: @abhishektiwari, @idoby
Archive: 10.5281/zenodo.11565998

Status

Status badge code:

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

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@abhishektiwari & @Ethan-CS & @idoby, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @vissarion know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @idoby

📝 Checklist for @abhishektiwari

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-03-15T09:31:57Z

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editorialbot · 2024-03-15T09:32:16Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1453.1 files/s, 145188.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            25            385            431           2047
Markdown                         2            174              0            489
TeX                              1             14              0            335
Maven                            1             10             17            294
XMI                             12              0              0            294
XML                              4              0              0            274
YAML                             1              1              4             18
JSON                             2              0              0              9
-------------------------------------------------------------------------------
SUM:                            48            584            452           3760
-------------------------------------------------------------------------------

Commit count by author:

    37	Dominik Grzelak

editorialbot · 2024-03-15T09:32:20Z

Paper file info:

📄 Wordcount for paper.md is 1079

✅ The paper includes a Statement of need section

editorialbot · 2024-03-15T09:32:21Z

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot · 2024-03-15T09:32:24Z

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

- No DOI given, and none found for title: EMF: Eclipse Modeling Framework
- No DOI given, and none found for title: The Space and Motion of Communicating Agents
- No DOI given, and none found for title: Principles of Model Checking
- No DOI given, and none found for title: Bigraphical Domain-specific Language (BDSL): User ...
- No DOI given, and none found for title: The GrGen.NET User Manual: Refers to GrGen.NET Rel...
- No DOI given, and none found for title: A SAT Based Algorithm for the Matching Problem in ...
- No DOI given, and none found for title: A CSP Implementation of the Bigraph Embedding Prob...
- No DOI given, and none found for title: Bigraph Ecore Metamodel (BEM): An EMOF-Compliant S...
- No DOI given, and none found for title: ISO/IEC 19508:2014 Information technology - Object...
- No DOI given, and none found for title: yFiles
- No DOI given, and none found for title: yComp

INVALID DOIs

- None

editorialbot · 2024-03-15T09:33:10Z

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

idoby · 2024-03-15T09:33:35Z

Review checklist for @idoby

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/bigraph-toolkit-suite/bigraphs.grgen-bigraphs?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@PioBeat) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

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 functionality 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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

abhishektiwari · 2024-03-16T02:02:24Z

Review checklist for @abhishektiwari

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/bigraph-toolkit-suite/bigraphs.grgen-bigraphs?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@PioBeat) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

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 functionality 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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

vissarion · 2024-04-25T08:29:17Z

Hello reviewers @abhishektiwari, @Ethan-CS, @idoby
Any updates on your progress?

vissarion · 2024-05-14T10:28:50Z

Hello @abhishektiwari, @Ethan-CS, @idoby kind reminder to provide some feedback on your review progress.

abhishektiwari · 2024-05-14T10:50:14Z

@vissarion Thanks for the nudge. I will aim to provide first feedback mid next week.

Ethan-CS · 2024-05-14T11:22:42Z

Thanks for the reminder - really sorry about the delay, I’ve been out of action due to illness for a while but getting back to it now I’m out of hospital. Will keep in touch, aiming to have finished by end of next week. On 14 May 2024, at 11:29, Vissarion Fisikopoulos ***@***.***> wrote: Hello @abhishektiwari<https://github.com/abhishektiwari>, @Ethan-CS<https://github.com/Ethan-CS>, @idoby<https://github.com/idoby> kind reminder to provide some feedback on your review progress. — Reply to this email directly, view it on GitHub<#6491 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARIYWRTWQSJBBLGVUH6QGJTZCHRPTAVCNFSM6AAAAABEXU36XGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBZHA2DGMRZGU>. You are receiving this because you were mentioned.Message ID: ***@***.***>

idoby · 2024-05-14T13:18:51Z

Hi, thanks for the reminder!

While this is well outside my field of expertise, just looking at the code it seems that this is a rather thin tool built on top of the GrGen framework. Can the author please explain why this package represents the results of significant scholarly effort as JOSS requires? It seems to me that if this code was written as part of a research paper on bigraphs, it might belong there rather than be published as a stand-alone general-use tool or library.
Furthermore, the "statement of need" section of the paper does not seem to present the need for this tool, rather it describes what it accomplishes. Hence, I am not convinced that this package should be published as a stand-alone tool.

I would appreciate it if the author could clarify these points.

PioBeat · 2024-05-16T11:11:26Z

Sure, I will be glad to clarify the purpose of this tool!

Note that the present tool paper is part of another journal paper entitled "Efficient Bigraph Rewriting using GrGen.NET" submitted for review to ACM Formal Aspects of Computing, where the full mathematical details are given on how the method actually works that is implemented as presented here for JOSS.
That is, the tool is a usable evaluation in form of a library and command-line tool.
I could provide the manuscript to the reviewers upon request.
While the code size is relatively small, the crucial and difficult part was the translation of the so-called relative pushout (RPO) rewrite semantics of bigraphs to the so-called single pushout (SPO) approach.
These are two different category-theoretic approaches to graph rewriting with different properties.
A side effect of developing such translation was the implementation of so-called tracking rules for bigraphs, which are further useful for causal reasoning and synchronization between two models.

In the software engineering communities it is widely acknowledged that graphs are a appropriate underlying mathematical formalism for representing and analyzing software models, modeling languages, processes and systems.
An approach to model and analyze the dynamics of systems and processes is by using an approach called graph transformation systems.
The usefulness of graph transformation in addressing various challenges in general software engineering is extensively explicated in [EEPT06].
Especially the algebraic formalisms, i.e., algebraic graph transformations systems, prove valuable as a formal specification technique in distributed state-based systems.
Through the application of so-called graph transformation rules, computations and transitions can be effectively described by local transformation of states, which are represented as graphs.
A rule consists of a left-hand side, specifying the graph pattern that needs to be found in the host graph, and a right-hand side that describes how the matched graph elements are rewritten afterwards.
Then, rules are applied to the current graph as long as the left-hand side occurs in the graph.
In this way, a transition system can be created and expanded incrementally by repeating the procedure on all new states until no rule can be applied anymore.

However, graph transformation essentially refers to the subgraph isomorphism problem, and more specifically for bigraphs this is referred to finding the forest in a tree (see [BaMR14]), both are NP-complete.

That being said, implementing bigraph matching and rewriting using the transformation tool GrGen.NET is for the following reasons.
First, to supplement the currently sparsely available rewriting implementations for bigraphs by providing a working and efficient alternative, and second, to compare performance across these approaches in future work.
From a practical standpoint, usable bigraph tools are BigraphER [SeCa16] and jLibBig [ChMP22], which solve bigraph matching as a Boolean satisfiability problem (SAT) and a Constraint satisfaction problem (CSP), respectively.
I believe that it is important to provide alternative rewrite implementation grounded on different techniques to make bigraphs available for future experiments and provide access to users with other tools.
A theory holds limited practical value in the absence of tools for its study and experimental evaluation.

I hope this clarifies some of your points. Should you have any further questions, I am more than happy to assist.

Kind regards,
Dominik

[EEPT06] Ehrig, Hartmut; Ehrig, Karsten; Prange, Ulrike; Taentzer, Gabriele: Fundamentals of Algebraic Graph Transformation, Monographs in Theoretical Computer Science. An EATCS Series. Berlin Heidelberg : Springer-Verlag, 2006 — ISBN 978-3-540-31187-4
[BaMR14] Bacci, Giorgio; Miculan, Marino; Rizzi, Romeo: Finding a Forest in a Tree. In: Maffei, M.; Tuosto, E. (Hrsg.): Trustworthy Global Computing, Lecture Notes in Computer Science : Springer Berlin Heidelberg, 2014 — ISBN 978-3-662-45917-1
[SeCa16] Sevegnani, Michele; Calder, Muffy: BigraphER: Rewriting and Analysis Engine for Bigraphs. In: Chaudhuri, S. ; Farzan, A. (Hrsg.): 28th International Conference on Computer Aided Verification. Bd. 9780. Toronto, Canada : Springer International Publishing, 2016 — ISBN 978-3-319-41539-0
[ChMP22] Chiapperini, Alessio ; Miculan, Marino ; Peressotti, Marco: Computing (optimal) embeddings of directed bigraphs. In: Science of Computer Programming Bd. 221 (2022)

idoby · 2024-05-17T06:11:23Z

Your explanation does sound to me like substantial contribution has been made to your field in the other paper, and hope that it gets accepted into the ACM journal.
However, as I understand it, JOSS requires that the software itself represent substantial effort and that it is likely to be used and cited as software. This package stands as the implementation of the algorithms in your other paper and therefore I believe users of your algorithms/code will likely cite the other paper, not the JOSS paper (as they should).

To conclude, while I applaud the scientific effort in developing the math, algorithms and implementation behind this package, I still have concerns regarding its fit for JOSS.

Since the JOSS guidelines are somewhat vague on this topic ("Co-publication of science, methods, and software"), I believe the decision should lie with the editor @vissarion.

vissarion · 2024-05-17T09:00:25Z

@idoby thank you for starting this discussion and for your comments.
@PioBeat thank you for your detailed answer and for defending your submission.

I will first share my point of view with the editorial team and ask for feedback and I will come back to you with the result of the discussions.

vissarion · 2024-05-17T09:00:32Z

@editorialbot query scope

editorialbot · 2024-05-17T09:00:34Z

Submission flagged for editorial review.

vissarion · 2024-05-21T07:40:40Z

@idoby @PioBeat I have some news regarding the query scope.

I am convinced (and other JOSS editors agree) that in this case the method and the software can be considered are separate contributions. The software seems to address specific software challenges, it contains useful sample data for testing and evaluation and comes with detailed instructions.

Thus, I will remove the query-scope tag and we could continue the review process. @idoby is this OK with you?

idoby · 2024-05-21T07:42:33Z

Sure, I will continue my review then.

PioBeat · 2024-06-11T10:23:54Z

Done @vissarion

vissarion · 2024-06-11T11:22:21Z

@editorialbot set 10.5281/zenodo.11565998 as archive

editorialbot · 2024-06-11T11:22:23Z

Done! archive is now 10.5281/zenodo.11565998

vissarion · 2024-06-11T11:22:45Z

@editorialbot set v1.2.0 as version

editorialbot · 2024-06-11T11:22:48Z

Done! version is now v1.2.0

vissarion · 2024-06-11T11:22:59Z

@editorialbot recommend-accept

editorialbot · 2024-06-11T11:23:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-06-11T11:23:26Z

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

- No DOI given, and none found for title: EMF: Eclipse Modeling Framework
- No DOI given, and none found for title: The Space and Motion of Communicating Agents
- No DOI given, and none found for title: Principles of Model Checking
- No DOI given, and none found for title: Bigraphical Domain-specific Language (BDSL): User ...
- No DOI given, and none found for title: The GrGen.NET User Manual: Refers to GrGen.NET Rel...
- No DOI given, and none found for title: A SAT Based Algorithm for the Matching Problem in ...
- No DOI given, and none found for title: A CSP Implementation of the Bigraph Embedding Prob...
- No DOI given, and none found for title: Bigraph Ecore Metamodel (BEM): An EMOF-Compliant S...
- No DOI given, and none found for title: ISO/IEC 19508:2014 Information technology - Object...
- No DOI given, and none found for title: yFiles
- No DOI given, and none found for title: yComp

INVALID DOIs

- None

editorialbot · 2024-06-11T11:24:25Z

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5482, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-06-11T14:45:01Z

@PioBeat - As track editor, I've now proofread your paper. I've suggested a lot of changes in bigraph-toolkit-suite/bigraphs.grgen-bigraphs#5. Please merge this or let me know what you disagree with, then we can generate another proof as a final check and then publish the work.

danielskatz · 2024-06-11T18:22:38Z

@editorialbot recommend-accept

editorialbot · 2024-06-11T18:22:40Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-06-11T18:23:08Z

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

- No DOI given, and none found for title: EMF: Eclipse Modeling Framework
- No DOI given, and none found for title: The Space and Motion of Communicating Agents
- No DOI given, and none found for title: Principles of Model Checking
- No DOI given, and none found for title: Bigraphical Domain-specific Language (BDSL): User ...
- No DOI given, and none found for title: The GrGen.NET User Manual: Refers to GrGen.NET Rel...
- No DOI given, and none found for title: A SAT Based Algorithm for the Matching Problem in ...
- No DOI given, and none found for title: A CSP Implementation of the Bigraph Embedding Prob...
- No DOI given, and none found for title: Bigraph Ecore Metamodel (BEM): An EMOF-Compliant S...
- No DOI given, and none found for title: ISO/IEC 19508:2014 Information technology - Object...
- No DOI given, and none found for title: yFiles
- No DOI given, and none found for title: yComp

INVALID DOIs

- None

editorialbot · 2024-06-11T18:24:48Z

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5487, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-06-11T18:26:29Z

@PioBeat - please take a look at this proof and confirm it looks ok. I will also look at it.

PioBeat · 2024-06-11T18:44:10Z

Dear @danielskatz Thank you very much for the editing. I have pushed also a small typo fix.
I do not have anything to add as far as I can see - so I confirm it looks ok.

danielskatz · 2024-06-11T19:07:03Z

Thanks for catching that.

danielskatz · 2024-06-11T19:07:08Z

@editorialbot accept

editorialbot · 2024-06-11T19:07:10Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-06-11T19:14:27Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Grzelak
  given-names: Dominik
  orcid: "https://orcid.org/0000-0001-6334-2356"
contact:
- family-names: Grzelak
  given-names: Dominik
  orcid: "https://orcid.org/0000-0001-6334-2356"
doi: 10.5281/zenodo.11565998
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Grzelak
    given-names: Dominik
    orcid: "https://orcid.org/0000-0001-6334-2356"
  date-published: 2024-06-11
  doi: 10.21105/joss.06491
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6491
  title: "BiGGer: A Model Transformation Tool written in Java for
    Bigraph Rewriting in GrGen.NET"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06491"
  volume: 9
title: "BiGGer: A Model Transformation Tool written in Java for Bigraph
  Rewriting in GrGen.NET"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-06-11T19:14:37Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-06-11T19:14:38Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06491 joss-papers#5490
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06491
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2024-06-11T19:30:44Z

Congratulations to @PioBeat (Dominik Grzelak) on your publication!!

And thanks to @abhishektiwari and @idoby for reviewing, and to @vissarion for editing!
JOSS depends on volunteers and we couldn't do this without you

editorialbot · 2024-06-11T19:30:46Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06491/status.svg)](https://doi.org/10.21105/joss.06491)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06491">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06491/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06491/status.svg
   :target: https://doi.org/10.21105/joss.06491

This is how it will look in your documentation:

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editorialbot added Java review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Mar 15, 2024

editorialbot assigned vissarion Mar 15, 2024

editorialbot mentioned this issue Mar 15, 2024

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

Closed

editorialbot added the query-scope Submissions of uncertain scope for JOSS label May 17, 2024

vissarion removed the query-scope Submissions of uncertain scope for JOSS label May 21, 2024

This was referenced May 25, 2024

Generate and publish Javadoc for BiGGer bigraph-toolkit-suite/bigraphs.grgen-bigraphs#1

Closed

Provide single Dockerfile with Mono, GrGen.NET, and BiGGer bigraph-toolkit-suite/bigraphs.grgen-bigraphs#2

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 11, 2024

editorialbot added accepted published Papers published in JOSS labels Jun 11, 2024

danielskatz closed this as completed Jun 11, 2024

editorialbot mentioned this issue Jan 15, 2025

[PRE REVIEW]: Pointcloud: Implementation of point clouds as graphs in the 3-d plant modeling platform GroIMP #7669

Closed

editorialbot mentioned this issue May 4, 2025

[PRE REVIEW]: Jangular: A Full-Stack Framework for Java and Angular Integration #8159

Closed

[REVIEW]: BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET #6491

[REVIEW]: BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET #6491

Comments

editorialbot commented Mar 15, 2024 • edited Loading

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idoby commented Mar 15, 2024 • edited Loading

Review checklist for @idoby

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abhishektiwari commented Mar 16, 2024 • edited Loading

Review checklist for @abhishektiwari

Conflict of interest

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General checks

Functionality

Documentation

Software paper

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editorialbot commented Mar 15, 2024 •

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