Skip to content

[REVIEW]: FAME-Core: An open Framework for distributed Agent-based Modelling of Energy systems #5087

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
editorialbot opened this issue Jan 19, 2023 · 58 comments
Assignees
Labels
accepted Java published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 3 (PE) Physics and Engineering

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Jan 19, 2023

Submitting author: @KriNiTi (Kristina Nienhaus)
Repository: https://gitlab.com/fame-framework/fame-core
Branch with paper.md (empty if default branch): 86-publish-paper
Version: v1.4.2
Editor: @fraukewiese
Reviewers: @xtruan, @pgranato
Archive: 10.5281/zenodo.7755760

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/90d9042b73c4337a71b0831b81b0b94c"><img src="https://joss.theoj.org/papers/90d9042b73c4337a71b0831b81b0b94c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/90d9042b73c4337a71b0831b81b0b94c/status.svg)](https://joss.theoj.org/papers/90d9042b73c4337a71b0831b81b0b94c)

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

@xtruan & @pgranato, 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 @fraukewiese 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 @pgranato

📝 Checklist for @xtruan

@editorialbot
Copy link
Collaborator Author

Hello humans, 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
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.88  T=0.20 s (964.8 files/s, 90787.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                           170           2040           2164          12510
XML                             10              0              0            580
Markdown                         9             89              0            324
Maven                            1             26              1            264
TeX                              1              9              0             92
YAML                             2              8             12             43
-------------------------------------------------------------------------------
SUM:                           193           2172           2177          13813
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 1238

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.1155/2017/7494313 is OK
- 10.1155/2017/1967645 is OK
- 10.1016/j.rser.2015.12.169 is OK
- 10.3390/en13153920 is OK
- 10.1016/j.energy.2016.03.038 is OK
- 10.1007/s10462-009-9105-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

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

@pgranato
Copy link

pgranato commented Jan 25, 2023

Review checklist for @pgranato

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

General checks

  • Repository: Is the source code for this software available at the https://gitlab.com/fame-framework/fame-core?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@KriNiTi) 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?

@xtruan
Copy link

xtruan commented Jan 29, 2023

Review checklist for @xtruan

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

General checks

  • Repository: Is the source code for this software available at the https://gitlab.com/fame-framework/fame-core?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@KriNiTi) 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?

@pgranato
Copy link

pgranato commented Feb 1, 2023

In general I find it difficult to review the project FAME-code in itself as it should be reviewed and analyzed taking into account the entire FAME-framework.

I have a few comments or questions related to the review items.

  • Contribution and authorship: Has the submitting author (@KriNiTi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I'm assuming that the submitting author (KriNiTi) is actually Kristina Nienhaus, but this is just a wild guess, since the GitHub account doesn't provide additional identification elements.
Most contributions to the codebese are by Christoph Schimeczek, which is also first author of the paper.

  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised."
I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers.

  • Installation: Does installation proceed as outlined in the documentation?

In general the installation is well documented and the project follows industrial standards. I managed to install FAME-core and, as suggested, FAME-demo.
I just notice that the file PrepareToInstallFameCore.launch, referenced by installation instructions is not present.

  • Functionality: Have the functional claims of the software been confirmed?

The FAME-demo shows basic functional features of the the software. An extensive analysis should be carried on to assess every aspect of the claimed functionalities. It's important to take into account that FAME-core is part of a broader software suite, part of which is currently under review for JOSS.

  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

The claimed performace are basically the same claimed on #5041
Since the project has been submited split in sevaral different papares it's hard to evaluate performances claims of the core package alone.

  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

I guess that the AMIRIS project under review on #5041 should be considered a real-world analysis problem. But since we are here reviewing FAME-code I guess at least a more explicit reference to AMIRIS should be made. The FAME-demo project is also a good usage example (even though a not real-world one).

  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

There is a wiki shared by all the projects of the FAME suite (https://gitlab.com/fame-framework/wiki/-/wikis/home).
The wiki is certainly clear and complete to a satisfactory level.

  • State of the field: Do the authors describe how this software compares to other commonly-used packages?

Authors list several other ABM frameworks and claim that they evaluated more than 40 other software but beside that there is no proper comparison. That said, personally, I don't think there is the strict need of an analytical comparison to justify the existence of a new ABM framework and therefore I judge the requirement fulfilled but nonetheless I pointed this out for the sake of the public discussion.

Last note.
In the context of the review #4958 FAME-Io, the paper has been modified to include an UML diagram replacing the diagram previously used in common with the one used in FAME-Core. My opinion is that both diagrams convey useful information and both should be used.

@fraukewiese
Copy link

@pgranato : Thanks for your effort so far. Regarding your question "The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised."
I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers."

I think this could be rather crosschecked by reviewers of #5041 .

@fraukewiese
Copy link

@KriNiTi : Please let us know what you think about the comments by @pgranato

@dlr-cjs
Copy link

dlr-cjs commented Feb 7, 2023

Dear @pgranato & @fraukewiese

thank you for your comments. Please find our response below:

  • Contribution and authorship: Has the submitting author (@KriNiTi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I'm assuming that the submitting author (KriNiTi) is actually Kristina Nienhaus, but this is just a wild guess, since the GitHub account doesn't provide additional identification elements. Most contributions to the codebese are by Christoph Schimeczek, which is also first author of the paper.

Kristina Nienhaus was leading the software project in which the original FAME code was created (originally not hosted on Gitlab). Most of the code was indeed written by me (Christoph Schimeczek). Kristina submitted the paper to JOSS on my behalf as I was leaving for a longer period of holidays just days before we got clearance to submit it. I am sorry if this latter issue caused confusion. I will serve as contact person from now on.

  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised." I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers.

We agree that it makes sense to consider the general runtime of AMIRIS as original result of the AMIRIS paper. However, we originally intended to make performance claims for FAME-Core regarding “low overhead” & “parallelization efficiency” in this paper using AMIRIS as an example. Since FAME-Core is the execution library of AMIRIS, the former is in fact co-responsible for its runtime. If you think this is not appropriate or confusing to keep it that way, we suggest the following to amend it: we could provide a dedicated performance testing suite for FAME-Core if you would be willing to verify our claims (Please note that this requires open-mpi compiled with Java)? If you think you could check that, we would provide such a suite of tests to measure parallelization efficiency and overhead of FAME - although it might take a few days to write that suite...

  • Installation: Does installation proceed as outlined in the documentation?

In general the installation is well documented and the project follows industrial standards. I managed to install FAME-core and, as suggested, FAME-demo. I just notice that the file PrepareToInstallFameCore.launch, referenced by installation instructions is not present.

Thanks for pointing this out. The mentioned file & tedious setup process is no longer required. We updated the README accordingly (as newer information was only available on the Wiki).

  • Functionality: Have the functional claims of the software been confirmed?

The FAME-demo shows basic functional features of the the software. An extensive analysis should be carried on to assess every aspect of the claimed functionalities. It's important to take into account that FAME-core is part of a broader software suite, part of which is currently under review for JOSS.

FAME-demo already uses most functional features of FAME-Core, including scheduling, messaging, input & output management. Do you require further demonstration of functionalities? If so, we would be happy to include additional examples, code or agents within the FAME-Demo project to demonstrate FAME-Core functionality.

  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

The claimed performace are basically the same claimed on #5041 Since the project has been submited split in sevaral different papares it's hard to evaluate performances claims of the core package alone.

Our original idea was not to make claims about FAME-Io or AMIRIS, but to hint at the low overhead of FAME-Core and its parallelizability (see also our comment at Reproducibility). We take this important hint to distinguish more clearly between performance claims for FAME-Core and runtime of FAME-Io or AMIRIS. To validate that FAME-Core is fast, precompiled input files could be used to - thus avoiding the runtime of FAME-Io to interfere. A dedicated suite of tests could allow comparison of runtime with / without FAME-Core. We would prepare such a test suite if you think it makes sense.

  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

I guess that the AMIRIS project under review on #5041 should be considered a real-world analysis problem. But since we are here reviewing FAME-code I guess at least a more explicit reference to AMIRIS should be made. The FAME-demo project is also a good usage example (even though a not real-world one).

We plan to have a direct reference to JOSS paper of AMIRIS currently under review #5041. The idea is to publish all three papers simultaneously, such that they directly refer to each other. Besides that, would you recommend a longer text describing AMIRIS in the FAME-Core paper as well? Should we add further references to peer-reviewed applications of AMIRIS or do you think the current text suffices?

  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

There is a wiki shared by all the projects of the FAME suite (https://gitlab.com/fame-framework/wiki/-/wikis/home). The wiki is certainly clear and complete to a satisfactory level.

We also want to point out the API documentation. Since it was easy to miss we added a corresponding badge in the repository.

  • State of the field: Do the authors describe how this software compares to other commonly-used packages?

Authors list several other ABM frameworks and claim that they evaluated more than 40 other software but beside that there is no proper comparison. That said, personally, I don't think there is the strict need of an analytical comparison to justify the existence of a new ABM framework and therefore I judge the requirement fulfilled but nonetheless I pointed this out for the sake of the public discussion.

We have this comparison available and could add text & tables. However, we originally thought this might blow up the paper and would be out of scope for a JOSS publication. Would you recommend a) including texts, tables and references to other frameworks, b) keep the text as is, or c) drop the reference to other frameworks completely?

Last note. In the context of the review #4958 FAME-Io, the paper has been modified to include an UML diagram replacing the diagram previously used in common with the one used in FAME-Core. My opinion is that both diagrams convey useful information and both should be used.

Do you think we should include both diagrams in this paper of FAME-Core, or would you recommend to keep the current diagram, thus complementing the FAME-Io paper #4958?

@pgranato
Copy link

pgranato commented Feb 7, 2023

Dear @pgranato & @fraukewiese

thank you for your comments. Please find our response below:

  • Contribution and authorship: Has the submitting author (@KriNiTi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I'm assuming that the submitting author (KriNiTi) is actually Kristina Nienhaus, but this is just a wild guess, since the GitHub account doesn't provide additional identification elements. Most contributions to the codebese are by Christoph Schimeczek, which is also first author of the paper.

Kristina Nienhaus was leading the software project in which the original FAME code was created (originally not hosted on Gitlab). Most of the code was indeed written by me (Christoph Schimeczek). Kristina submitted the paper to JOSS on my behalf as I was leaving for a longer period of holidays just days before we got clearance to submit it. I am sorry if this latter issue caused confusion. I will serve as contact person from now on.

That's fine for me. Checked out this point.

  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

The paper claims "In single-core mode, FAME-Core executes the AMIRIS model with low overhead – performing a simulation of the German wholesale electricity market for one year in hourly resolution on a desktop computer within about 20 seconds. In multi-core mode, FAME demonstrated high parallelisation efficiency for a setup of 16 computationally heavy agents: Computation wall time was roughly proportional to 1/𝑛 as 𝑛 ∈ 1, 2, 4, 8 cores were utilised." I'm not sure if, by the standard of JOSS, this is considered original result and hence should be cross checked by reviewers.

We agree that it makes sense to consider the general runtime of AMIRIS as original result of the AMIRIS paper. However, we originally intended to make performance claims for FAME-Core regarding “low overhead” & “parallelization efficiency” in this paper using AMIRIS as an example. Since FAME-Core is the execution library of AMIRIS, the former is in fact co-responsible for its runtime. If you think this is not appropriate or confusing to keep it that way, we suggest the following to amend it: we could provide a dedicated performance testing suite for FAME-Core if you would be willing to verify our claims (Please note that this requires open-mpi compiled with Java)? If you think you could check that, we would provide such a suite of tests to measure parallelization efficiency and overhead of FAME - although it might take a few days to write that suite...

Unfortunately I will not be able to check the suggested performance testing suite. I agree with @fraukewiese that this claim can be cross checked by AMIRIS on #5041

  • Installation: Does installation proceed as outlined in the documentation?

In general the installation is well documented and the project follows industrial standards. I managed to install FAME-core and, as suggested, FAME-demo. I just notice that the file PrepareToInstallFameCore.launch, referenced by installation instructions is not present.

Thanks for pointing this out. The mentioned file & tedious setup process is no longer required. We updated the README accordingly (as newer information was only available on the Wiki).

Ok, checked.

  • Functionality: Have the functional claims of the software been confirmed?

The FAME-demo shows basic functional features of the the software. An extensive analysis should be carried on to assess every aspect of the claimed functionalities. It's important to take into account that FAME-core is part of a broader software suite, part of which is currently under review for JOSS.

FAME-demo already uses most functional features of FAME-Core, including scheduling, messaging, input & output management. Do you require further demonstration of functionalities? If so, we would be happy to include additional examples, code or agents within the FAME-Demo project to demonstrate FAME-Core functionality.

  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

The claimed performace are basically the same claimed on #5041 Since the project has been submited split in sevaral different papares it's hard to evaluate performances claims of the core package alone.

Our original idea was not to make claims about FAME-Io or AMIRIS, but to hint at the low overhead of FAME-Core and its parallelizability (see also our comment at Reproducibility). We take this important hint to distinguish more clearly between performance claims for FAME-Core and runtime of FAME-Io or AMIRIS. To validate that FAME-Core is fast, precompiled input files could be used to - thus avoiding the runtime of FAME-Io to interfere. A dedicated suite of tests could allow comparison of runtime with / without FAME-Core. We would prepare such a test suite if you think it makes sense.

  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

I guess that the AMIRIS project under review on #5041 should be considered a real-world analysis problem. But since we are here reviewing FAME-code I guess at least a more explicit reference to AMIRIS should be made. The FAME-demo project is also a good usage example (even though a not real-world one).

We plan to have a direct reference to JOSS paper of AMIRIS currently under review #5041. The idea is to publish all three papers simultaneously, such that they directly refer to each other. Besides that, would you recommend a longer text describing AMIRIS in the FAME-Core paper as well? Should we add further references to peer-reviewed applications of AMIRIS or do you think the current text suffices?

I think that having the three papers published simultaneously (and referencing each other) solves much of this questions and should be enough for the readers to understand the general concepts of the framework, functionalities and performance claims.

  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

There is a wiki shared by all the projects of the FAME suite (https://gitlab.com/fame-framework/wiki/-/wikis/home). The wiki is certainly clear and complete to a satisfactory level.

We also want to point out the API documentation. Since it was easy to miss we added a corresponding badge in the repository.

Thanks. Checked.

  • State of the field: Do the authors describe how this software compares to other commonly-used packages?

Authors list several other ABM frameworks and claim that they evaluated more than 40 other software but beside that there is no proper comparison. That said, personally, I don't think there is the strict need of an analytical comparison to justify the existence of a new ABM framework and therefore I judge the requirement fulfilled but nonetheless I pointed this out for the sake of the public discussion.

We have this comparison available and could add text & tables. However, we originally thought this might blow up the paper and would be out of scope for a JOSS publication. Would you recommend a) including texts, tables and references to other frameworks, b) keep the text as is, or c) drop the reference to other frameworks completely?

I guess that a short paragraph or a small table that briefly describes the comparison with the few you closely analyzed should be added replacing "We closely examined, e.g., Jade, MASS, Repast and Akka."

Last note. In the context of the review #4958 FAME-Io, the paper has been modified to include an UML diagram replacing the diagram previously used in common with the one used in FAME-Core. My opinion is that both diagrams convey useful information and both should be used.

Do you think we should include both diagrams in this paper of FAME-Core, or would you recommend to keep the current diagram, thus complementing the FAME-Io paper #4958?

Since the paper are going to be published together I recommend to keep the current diagram.

@fraukewiese
Copy link

fraukewiese commented Feb 8, 2023

@dlr-cjs
I fully agree with @pgranato regarding his suggestion:
"I guess that a short paragraph or a small table that briefly describes the comparison with the few you closely analyzed should be added replacing "We closely examined, e.g., Jade, MASS, Repast and Akka.""
It is a very important point to clarify why the software could not be build upon an existing framework but had to be built from scratch, thus some more explanation in the paper are required.

@dlr-cjs
Copy link

dlr-cjs commented Feb 14, 2023

Dear @fraukewiese & @pgranato,

we rewrote the "Statement of need" to include a more detailed examination of the frameworks we assessed and why we decided to create FAME. We hope that our changes address your comments appropriately.

@pgranato
Copy link

@editorialbot generate pdf

@pgranato
Copy link

@editorialbot commands

@editorialbot
Copy link
Collaborator Author

Hello @pgranato, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

@editorialbot
Copy link
Collaborator Author

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

@fraukewiese
Copy link

fraukewiese commented Feb 20, 2023

@pgranato : Do you think your comment regarding the statement of need it is addressed adequately?

@pgranato
Copy link

Hi @fraukewiese, yes I think that this version of the article clarifies sufficiently the state of the field and the need of a new software.
Regarding the other two open points, namely Reproducibility and Performance: I think I did what possibile to check the points and I'm personally convinced that the requests are satisfied. Since we discussed that this points could be also cross-checked by reviewers of #5041 and they have been independently verified by reviewers of that submission I marked as checked also here.

@fraukewiese
Copy link

@pgranato : Thank you very much for your thorough review!

We will now wait for the further review by @xtruan

@fraukewiese
Copy link

Hi @xtruan : Could you update us on how the review is going? Thanks a lot :)

@xtruan
Copy link

xtruan commented Mar 8, 2023

Hey sorry for being the slowpoke here, I will get my review completed by the end of this week!

@editorialbot
Copy link
Collaborator Author

Done! Archive is now 10.5281/zenodo.7755760

@fraukewiese
Copy link

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.1155/2017/7494313 is OK
- 10.1155/2017/1967645 is OK
- 10.1016/j.rser.2015.12.169 is OK
- 10.3390/en13153920 is OK
- 10.1016/j.energy.2016.03.038 is OK
- 10.1007/s10462-009-9105-x is OK

MISSING DOIs

- None

INVALID DOIs

- 10.21105/joss.04958 is INVALID
- 10.21105/joss.05041 is INVALID

@fraukewiese
Copy link

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.1155/2017/7494313 is OK
- 10.1155/2017/1967645 is OK
- 10.1016/j.rser.2015.12.169 is OK
- 10.3390/en13153920 is OK
- 10.1016/j.energy.2016.03.038 is OK
- 10.1007/s10462-009-9105-x is OK

MISSING DOIs

- None

INVALID DOIs

- 10.21105/joss.04958 is INVALID
- 10.21105/joss.05041 is INVALID

@editorialbot
Copy link
Collaborator Author

👋 @openjournals/pe-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#4118, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 12, 2023
@kyleniemeyer
Copy link

Hello @Krinit @dlr-cjs, as with the other papers, I made some formatting changes to the paper: https://gitlab.com/fame-framework/fame-core/-/merge_requests/69

Could you merge these?

@dlr-cjs
Copy link

dlr-cjs commented Apr 17, 2023

Thank you @kyleniemeyer for your formatting changes. I merge them as requested.

@kyleniemeyer
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@kyleniemeyer
Copy link

@editorialbot accept

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

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: Schimeczek
  given-names: Christoph
  orcid: "https://orcid.org/0000-0002-0791-9365"
- family-names: Deissenroth-Uhrig
  given-names: Marc
  orcid: "https://orcid.org/0000-0002-9103-418X"
- family-names: Frey
  given-names: Ulrich
  orcid: "https://orcid.org/0000-0002-9803-1336"
- family-names: Fuchs
  given-names: Benjamin
  orcid: "https://orcid.org/0000-0002-7820-851X"
- family-names: Ghazi
  given-names: A. Achraf El
  orcid: "https://orcid.org/0000-0001-5064-9148"
- family-names: Wetzel
  given-names: Manuel
  orcid: "https://orcid.org/0000-0001-7838-2414"
- family-names: Nienhaus
  given-names: Kristina
  orcid: "https://orcid.org/0000-0003-4180-6767"
contact:
- family-names: Schimeczek
  given-names: Christoph
  orcid: "https://orcid.org/0000-0002-0791-9365"
doi: 10.5281/zenodo.7755760
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schimeczek
    given-names: Christoph
    orcid: "https://orcid.org/0000-0002-0791-9365"
  - family-names: Deissenroth-Uhrig
    given-names: Marc
    orcid: "https://orcid.org/0000-0002-9103-418X"
  - family-names: Frey
    given-names: Ulrich
    orcid: "https://orcid.org/0000-0002-9803-1336"
  - family-names: Fuchs
    given-names: Benjamin
    orcid: "https://orcid.org/0000-0002-7820-851X"
  - family-names: Ghazi
    given-names: A. Achraf El
    orcid: "https://orcid.org/0000-0001-5064-9148"
  - family-names: Wetzel
    given-names: Manuel
    orcid: "https://orcid.org/0000-0001-7838-2414"
  - family-names: Nienhaus
    given-names: Kristina
    orcid: "https://orcid.org/0000-0003-4180-6767"
  date-published: 2023-04-17
  doi: 10.21105/joss.05087
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5087
  title: "FAME-Core: An open Framework for distributed Agent-based
    Modelling of Energy systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05087"
  volume: 8
title: "FAME-Core: An open Framework for distributed Agent-based
  Modelling of Energy systems"

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
Copy link
Collaborator Author

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@editorialbot
Copy link
Collaborator Author

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

@editorialbot
Copy link
Collaborator Author

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05087 joss-papers#4133
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05087
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Apr 17, 2023
@kyleniemeyer
Copy link

Congratulations @KriNiTi and @dlr-cjs on your article's publication in JOSS!

Thanks so much to @xtruan and @pgranato for reviewing this, and @fraukewiese for editing.

@editorialbot
Copy link
Collaborator Author

🎉🎉🎉 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.05087/status.svg)](https://doi.org/10.21105/joss.05087)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05087">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05087/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05087/status.svg
   :target: https://doi.org/10.21105/joss.05087

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
accepted Java published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 3 (PE) Physics and Engineering
Projects
None yet
Development

No branches or pull requests

6 participants