Closed editorialbot closed 1 year ago
editorialbot
commented
2 years ago 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 commandsFor example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdfSoftware report:
github.com/AlDanial/cloc v 1.88 T=3.80 s (526.6 files/s, 123140.8 lines/s)
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JSON 237 901 0 145615
C++ 507 12457 12534 107762
Java 299 5564 4341 45546
C/C++ Header 451 5832 3174 22920
C# 202 2300 1122 20551
Markdown 33 3085 0 11785
Python 97 2233 1194 11675
CSS 10 270 108 9416
XML 23 13 39 8102
TeX 2 836 0 7157
CMake 43 497 933 5025
Protocol Buffers 44 509 330 3715
JavaScript 6 572 354 2550
Sass 13 26 24 1352
LESS 13 26 33 1343
Bourne Shell 4 51 205 1321
HTML 9 68 45 1131
SVG 3 0 1 803
MSBuild script 1 0 0 261
DOS Batch 3 19 0 100
Dockerfile 1 9 2 51
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gitinspector failed to run statistical information for the repositoryWordcount for paper.md is 1904
editorialbot
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2 years ago :point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
editorialbot
commented
2 years ago Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1101/2020.05.19.20107201 is OK
- 10.1007/978-3-319-91467-1_19 is OK
- 10.1145/3357495.3357499 is OK
- 10.1007/s42399-019-00053-w is OK
- 10.1097/01.sla.0000234655.83517.56 is OK
- 10.1542/peds.2007-2902 is OK
- 10.1097/PCC.0b013e3181f52b2f is OK
- 10.1016/j.anclin.2007.03.009 is OK
- 10.1016/j.jpedsurg.2008.02.033 is OK
- 10.7861/fhj.2019-0036 is OK
- 10.30476/jamp.2020.86070.1213 is OK
MISSING DOIs
- 10.23919/annsim55834.2022.9859325 may be a valid DOI for title: Implementation of a Dynamic and Extensible Mechanical Ventilator Model for Real-Time Physiological Simulation
INVALID DOIs
- None
prashjha
commented
2 years ago Dear @alexrockhill and @vaniisgh, please read the first couple of comments in this thread and create your review checklist. You can read the reviewer guidelines here. Also, you can browse the closed "REVIEW" issues on the "joss-reviews" repository to get some ideas on how to complete the reviews. Good luck!
vaniisgh
commented
1 year ago 
alexrockhill
commented
1 year ago alexrockhill
commented
1 year ago In relation to this checklist item
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
and this conversation in pre-review:
Could you say more about how this previous paper (from 2019) relates to this JOSS submission?
The 2019 paper was our first overview paper introducing pulse and its components. The JOSS submission focuses on our latest features not included in the 2019 paper, including the unity asset and unreal plugin, the ventilator and our hemorrhage improvements. These features show our advantages over other physiology engines.
In my opinion it's not clear from the title and summary of the publication that this smaller scope is the scope of the publication; it appears from reading the title and summary that this is the flagship publication for this software. Since, the 2019 publication is already titled as the flagship publication for the software, this seems confusing and potentially self-plagiarizing to me. I think this could easily be resolved by clarifying scope in the title and summary, perhaps by enumerating the new models that were added and focusing on them specifically instead of putting them in a list of "[r]ecent advances" that include items such as the COVID model published elsewhere. A nice way to handle this might be to think of a theme that ties "the unity asset and unreal plugin, the ventilator and our hemorrhage improvements" together as far as what the overarching goal(s) of the project have been in the last three years. Maybe 'low-latency, improved realism of hemorrhage and ventilator models in Pulse Physiology Engine' might make more sense, please make the title whatever you think is best though (as long as it is clear that it is not the flagship publication), I just thought it would be helpful to provide an example.
Also Figure 3 is reproduced from the 2019 publication almost identically without attribution; this figure should be compared to that publication directly (or this part should be removed and the focus shifted to the new modules).
EDIT: I guess just titling the manuscript after the latest version release would make the scope clear and then removing things in the summary that sound like it's the first/flagship publication and making it clear that this publication covers the newest version would be a smaller change that would also solve this issue.
alexrockhill
commented
1 year ago Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
I don't see in the README of https://gitlab.kitware.com/physiology/explorer or https://pulse.kitware.com/ any information about how to run the tests. Could you please point me to this information (and add it to the README) or add it if it does not exist? It looks like it may not be written yet from this source https://gitlab.kitware.com/physiology/engine/-/wikis/Creating%20a%20Unit%20Test which says "TODO".
alexrockhill
commented
1 year ago Overall, the authors provide a mature software tool to model cardiopulmonary function in healthy and disease states and with medical intervention that will be and is undoubtedly useful to a wide medical audience. The software is easy to install and I was able to test that the basic functionality works in the application. There are many possible extensions to the tool, such as new medical interventions or simulations of other aspects of physiology that can be measured, and while it doesn't appear that there are contributors outside the core group yet, documentation has been started on how to add contributors and grow the open-source project.
While the application is very well made and widely applicable, unfortunately it seems that to satisfy the checklist items for the review would require a major rewrite of the paper and major additions to the documentation that I think would be very helpful to the growth of Pulse in the long-term but may be onerous to complete for an expeditious publication. Here are the major points:
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- There are mostly empty headers in the API documentation (i.e. https://pulse.kitware.com/class_s_e_hemorrhage.html). Documenting this API seems like a very large undertaking but I think it would make the software much easier to contribute to, potentially enabling the number of contributors to grow.
Functionality: Have the functional claims of the software been confirmed?
- The main functionalities of the publication; modeling hemorrhage and intervention with a ventilator have been published elsewhere (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4106696 and https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9859325 respectively). I was unable to get a working version of Unity installed on my machine (running Ubuntu 22.04); the application crashed when I tried to run UnityHub, and since I want to focus my efforts on the software in this review, I have not continued to troubleshoot this so I was not able to verify that the Unity extension worked. Since the hemorrhage and ventilator models have already been published and the Unity and Unreal Engine extensions have not been published previously, those could be the main subject for publication but that is not the main focus of the paper as written. Otherwise, the last component mentioned was the
Automated Verification and Validation. While this is publishable, the main functionality of Pulse has already been published in 2019 and it is not clear that extensive tests and validation have been added since then. Thus, the scope of the functional claims of this manuscript may be limited to just the Unity and Unreal Engine extensions, although that is not how the manuscript is currently written, this should be clarified.
It's the policy of JOSS to make it easy so that if the software is developed well, the paper follows with minimal effort so I'm sorry to the authors that my review doesn't facilitate publication with minimal barriers, especially since the software works so well and seems widely useful. The software doesn't conform well to the review guidelines as written from my perspective but perhaps if it were rewritten to focus on the Unity asset and Unreal Engine plugin it could be suitable for publication in JOSS.
aaron-bray
commented
1 year ago Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
@alexrockhill
We have a utility script that runs various drivers built with Pulse Our home wiki documents this here: https://gitlab.kitware.com/physiology/engine/-/wikis/home
I need to update the How to perform verification and validation section
Basically, you want to ./run.sh DebugRun from your build/install/bin directory
This will run the one test case in this config file
When successful, you will have results
./install/bin/test_results/scenarios/patient/ folderTo run all tests, this takes several hours (and is multi threaded so it will kill your occupy your entire machine) which consists of automatically running
./run.sh CDMUnitTests./run.sh EngineUnitTests/run.sh ScenarioVerificationValidation is perfomed with
./run.sh SystemValidation
or
./run.sh PatientValidation
All of this can be done individually or via one call: ./run.sh tests
We also can copy any test line from the associated config files above, put it the DebugRun.config, to run those particular tests
for example, adding the line patient/TensionPneumothoraxBilateral.json = ScenarioTest to the bottom of the DebugRun.config will execute TensionPneumothoraxBilateral scenario when ./run.sh DebugRun is executed
Note that line references/executes this scenaio
aaron-bray
commented
1 year ago the software is developed well, the paper follows with minimal effort
@alexrockhill
I understand what you are saying here.
I think we could use JOSS to discuss various aspects (ex. hemorrhage updates, the mechanical ventilator, unity, unreal) of this version release. Does it seem feasible within JOSS, to publish a new JOSS article when we make a release? We could open by referencing our 2019 paper, then expanding on the major improvments. This would result in our repository would have multiple JOSS paper markdown files, for each time we publish. Are there other projects that work with JOSS this way? I am not sure if there are different guidlines for version release publications.
Thanks!
alexrockhill
commented
1 year ago I forgot that the guidelines specify that the publication can be a companion to a results paper (https://joss.readthedocs.io/en/latest/submitting.html) so I think I'll just review more thoroughly the examples and tutorials for the hemorrhage and ventilator models and I think that will satisfy the requirement of substantial scholarly effort beyond the publication for the development of the software.
alexrockhill
commented
1 year ago I think we could use JOSS to discuss various aspects (ex. hemorrhage updates, the mechanical ventilator, unity, unreal) of this version release. Does it seem feasible within JOSS, to publish a new JOSS article when we make a release? We could open by referencing our 2019 paper, then expanding on the major improvments. This would result in our repository would have multiple JOSS paper markdown files, for each time we publish. Are there other projects that work with JOSS this way? I am not sure if there are different guidlines for version release publications.
I'm not aware of projects that publish a new JOSS paper every major version release but I don't think it's against any rules or guidelines as far as I am aware. I think the main thing is to just make it clear what work the publication is covering and that it's been done since the last publication. Personally, I have published in JOSS for major new features rather than version releases and used the paper to describe the new functionality that may be added in one version but then smaller improvements and bug fixes are added in subsequent versions. Here is that paper from a larger software package that is a major module addition https://joss.theoj.org/papers/10.21105/joss.03897.
alexrockhill
commented
1 year ago A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Could the authors please add a bit more about the interaction between the hemorrhage and ventilator models and the existing functionality (e.g. giving medication) and how this could be used? This is covered in the introductory videos so those could be referenced but it would be nice to see a bit more about the use cases.
aaron-bray
commented
1 year ago Hey @alexrockhill
Just an FYI, I did not get to this over break (I actually had a break!) I am also busy prepping for our IMSH outing next week. (Drop by our booth if you are going!)
But After that, I will get all these items addressed!
Thanks for your time!
alexrockhill
commented
1 year ago @aaron-bray, I'm glad you had a good break!
I'm at the North American Neuromodulation Society (NANS) meeting this week so it was a bit much to do IMSH but best of luck at your booth!
prashjha
commented
1 year ago Hello @vaniisgh, how is the review progressing?
aaron-bray
commented
1 year ago Hi @alexrockhill @prashjha @vaniisgh
I updated the paper to be more oriented towards the Major Version Release submission category It should be around the 1000 word mark, I cut a little more detail to sections (~500 words) If you think it needs it and 1500 words is ok, I can integrate it back in (Its in the paper.full.md file if interested)
I am going to start improving our execution documentation as mentioned by Alex
Let me know if this draft is more in line with the release paper type
Thanks!
prashjha
commented
1 year ago Hello @vaniisgh, please let me know how far you are in finishing the review.
prashjha
commented
1 year ago Hi @vaniisgh, I have not heard from you for a long time, and your checklist has not changed in the last four months. If you are unable to review it, please let us know!
aaron-bray
commented
1 year ago @prashjha Should we get a new reviewer?
prashjha
commented
1 year ago @aaron-bray, yes. I have been trying to get in touch with @vaniisgh over her email too. I will invite new reviewers today.
prashjha
commented
1 year ago Hi @alcantarar, I think this JOSS submission is in your area of interest. Would you, by any chance, be interested and have time to review this submission? Please let me know. Also, if you need more information about the review process, I can help.
alcantarar
commented
1 year ago Hi, thanks for considering me for this review. Unfortunately I’m unavailable to review publications at this time.
R
On Mon, Apr 17, 2023 at 2:00 PM Prashant K. Jha @.***> wrote:
Hi @alcantarar https://github.com/alcantarar, I think this JOSS submission is in your area of interest. Would you, by any chance, be interested and have time to review this submission? Please let me know. Also, if you need more information about the review process, I can help.
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4929#issuecomment-1512077901, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJDMLEOTC5KR5XVT2QA5Y2LXBWVOLANCNFSM6AAAAAASABKCRY . You are receiving this because you were mentioned.Message ID: @.***>
prashjha
commented
1 year ago @alcantarar, no worries; thanks for quick reply.
prashjha
commented
1 year ago Hello @abhishektha, I am wondering if you could review this JOSS submission. I believe it is in your area of interest. If you need any information, please let me know. For more details about the review process, please check out this link.
aaron-bray
commented
1 year ago Hey @prashjha It seems like we are not having luck finding reviewers Should we look for more off your list or should I try to find one outside of that?
Thanks!
prashjha
commented
1 year ago Hi @aaron-bray, sorry for the delay. I will add myself as a reviewer and hope to finish the review in the next couple of weeks.
prashjha
commented
1 year ago @editorialbot help
editorialbot
commented
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editorialbot
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1 year ago @vaniisgh removed from the reviewers list!
editorialbot
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1 year ago I'm sorry human, I don't understand that. You can see what commands I support by typing:
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editorialbot
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1 year ago I'm sorry human, I don't understand that. You can see what commands I support by typing:
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prashjha
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1 year ago @editorialbot add me as reviewer
editorialbot
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1 year ago @prashjha added to the reviewers list!
prashjha
commented
1 year ago @editorialbot generate checklist
editorialbot
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1 year ago I'm sorry human, I don't understand that. You can see what commands I support by typing:
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prashjha
commented
1 year ago prashjha
commented
1 year ago Hi @alexrockhill, could you please provide an update on the progress of your review? Thanks!!
alexrockhill
commented
1 year ago @editorialbot generate pdf
alexrockhill
commented
1 year ago Hi @alexrockhill, could you please provide an update on the progress of your review? Thanks!!
My initial review is finished; I suggested minor revisions above. I need to look at the changes the authors made in response and and check the final items off the checklist.
editorialbot
commented
1 year ago :point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
alexrockhill
commented
1 year ago It doesn't look like all of the changes I suggested have been made yet so I'll hold off on reviewing those until then.
aaron-bray
commented
1 year ago Hey @prashjha I would like to rescind this submission. The version direction I chose for this paper was not the right way to go. I am going to look to resubmit feature specific papers associated with Pulse as mentioned by @alexrockhill
I have published in JOSS for major new features rather than version releases and used the paper to describe the new functionality that may be added in one version but then smaller improvements and bug fixes are added in subsequent versions.
Alex, thanks for all the feedback you provided. I hope to have a better paper submitted by the end of the year.
Thanks!
alexrockhill
commented
1 year ago Sounds good, happy to review if asked. Good luck @aaron-bray
prashjha
commented
1 year ago Hi @Kevin-Mattheus-Moerman, the author of this review wishes to withdraw the submission; see comment. Could you please help? Thanks, Prashant.
Kevin-Mattheus-Moerman
commented
1 year ago @aaron-bray @prashjha understood. I will now proceed to withdraw this submission.
Submitting author: !--author-handle-->@aaron-bray<!--end-author-handle-- (Aaron Bray) Repository: https://gitlab.kitware.com/physiology/engine Branch with paper.md (empty if default branch): publication/JOSS Version: v4.1.0 Editor: !--editor-->@prashjha<!--end-editor-- Reviewers: @alexrockhill, @prashjha Archive: Pending
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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
@alexrockhill & @vaniisgh, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @prashjha 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 ✨
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