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[PRE REVIEW]: Pulse Physiology Engine: A Computational Physiology Engine for Whole-Body Simulation #4647

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

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, @vaniisgh Managing EiC: Arfon Smith

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HTML: <a href="https://joss.theoj.org/papers/f28e96343ebb407cd458ac0e15439bd6"><img src="https://joss.theoj.org/papers/f28e96343ebb407cd458ac0e15439bd6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f28e96343ebb407cd458ac0e15439bd6/status.svg)](https://joss.theoj.org/papers/f28e96343ebb407cd458ac0e15439bd6)

Author instructions

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

@aaron-bray if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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editorialbot commented 2 years ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@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 commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=2.21 s (907.3 files/s, 212142.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
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           7155
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
-------------------------------------------------------------------------------
SUM:                          2001          35268          24439         408179
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1904

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
- 10.1007/s42399-019-00053-w is OK
- 10.1097/01.sla.0000234655.83517.56 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

- 10.1145/3357495.3357499 may be a valid DOI for title: Towards A Test and Validation Framework for Closed-Loop Physiology Management Systems for Critical and Perioperative Care
- 10.1542/9781610020862-part05-patient_safety may be a valid DOI for title: Patient Safety in the Pediatric Emergency Care Setting

INVALID DOIs

- None
arfon commented 2 years ago

Thanks for your submission to JOSS @aaron-bray. Could you say more about how this previous paper (from 2019) relates to this JOSS submission?

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

aaron-bray commented 2 years ago

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.

arfon commented 2 years ago

@aaron-bray – got it. Thanks. Is it possible/straightforward to link to these contributions directly, either as significant pull requests/contributions, a diff showing the changes since 2019 or something similar?

aaron-bray commented 2 years ago

@arfon We could add a link to our release section, and state the releases that our paper focus on

https://gitlab.kitware.com/physiology/engine/-/releases

danielskatz commented 2 years ago

@arfon - just a ping on this...

arfon commented 2 years ago

@arfon We could add a link to our release section, and state the releases that our paper focus on

https://gitlab.kitware.com/physiology/engine/-/releases

Yes, that sounds like a good idea (apologies for the delayed response here).

arfon commented 2 years ago

@aaron-bray – apologies for the delay here but we're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

arfon commented 2 years ago

@editorialbot invite @prashjha as editor

:wave: @prashjha – would you be willing to edit this submission for JOSS?

editorialbot commented 2 years ago

Invitation to edit this submission sent!

prashjha commented 2 years ago

@arfon thanks...I will be very interested in editing this.

prashjha commented 2 years ago

@editorialbot assign me as editor

editorialbot commented 2 years ago

Assigned! @prashjha is now the editor

prashjha commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

prashjha commented 2 years ago

@aaron-bray sorry for the delay; I was traveling and just came back. This is an excellent submission. It will be helpful if you could suggest a few potential reviewers for this submission. Thanks.

aaron-bray commented 2 years ago

Hi @prashjha I think anyone within the biomedical engineering / physiology domain would be applicable

prashjha commented 2 years ago

Thanks for the suggestions, @aaron-bray.

prashjha commented 2 years ago

Hi, @hofmannu; 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.

prashjha commented 2 years ago

Hello, @alexrockhill; I am looking for two reviewers for this JOSS submission. I think the submission is close to your interest areas. Is there a chance you could review this?

alexrockhill commented 2 years ago

Yes, I can review.

prashjha commented 2 years ago

Great, @alexrockhill. Thank you!!

prashjha commented 2 years ago

@editorialbot add @alexrockhill as reviewer

editorialbot commented 2 years ago

@alexrockhill added to the reviewers list!

prashjha commented 2 years ago

Hi @kostadus, would you be interested in reviewing this submission for JOSS? I believe this is in your area of interest. Please let me know!

alexrockhill commented 2 years ago

It looks like maybe their GitHub is inactivated @prashjha

aaron-bray commented 2 years ago

We use our own gitlab instance here:

Repository: https://gitlab.kitware.com/physiology/engine Branch with paper.md (empty if default branch): publication/JOSS

On Thu, Nov 10, 2022 at 7:25 PM Alex Rockhill @.***> wrote:

It looks like maybe their GitHub is inactivated @prashjha https://github.com/prashjha

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4647#issuecomment-1311073372, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGTUWH26WKOQ3JIUHR7Q7YLWHWG7HANCNFSM55QB3OJQ . You are receiving this because you were mentioned.Message ID: @.***>

alexrockhill commented 2 years ago

I meant the other reviewer, kostadus, that was meant to be tagged, sorry for any confusion @aaron-bray

aaron-bray commented 2 years ago

Oh! Ha!

No problem!

prashjha commented 1 year ago

@alexrockhill, yeah...probably it was active when I invited.

prashjha commented 1 year ago

Hi @vaniisgh, would you be interested in reviewing this submission for JOSS? I think it is in your area of interest. Please let me know!!

prashjha commented 1 year ago

Hello @VeroniqueLegrand, any chance you could review this submission for JOSS? It is in your area of interest. I can help with further details if you are interested. Please let me know!!

vaniisgh commented 1 year ago

i could help :)

prashjha commented 1 year ago

Awesome, @vaniisgh! Adding you as a reviewer now.

prashjha commented 1 year ago

@editorialbot add @vaniisgh as reviewer

editorialbot commented 1 year ago

@vaniisgh added to the reviewers list!

prashjha commented 1 year ago

Hi, @hofmannu and @VeroniqueLegrand; please ignore my invitation to review this submission. We now have two required reviewers.

prashjha commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4929.

VeroniqueLegrand commented 1 year ago

Hello,

Thank you for your interest. I am pretty busy these days. I will not have the time to do the review. Best regards,

Véronique

-- Véronique Legrand Software & IT engineer – HPC/HTC https://research.pasteur.fr/en/member/veronique-legrand/ HPC platform Institut Pasteur Paris Tel : 01 44 38 95 03 07 88 15 34 68

De : "Prashant K. Jha" @.> Répondre à : openjournals/joss-reviews @.> Date : lundi 14 novembre 2022 à 16:06 À : openjournals/joss-reviews @.> Cc : Véronique LEGRAND @.>, Mention @.***> Objet : Re: [openjournals/joss-reviews] [PRE REVIEW]: Pulse Physiology Engine: A Computational Physiology Engine for Whole-Body Simulation (Issue #4647)

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