[REVIEW]: svFSI: A Multiphysics Package for Integrated Cardiac Modeling

[whedon]

Submitting author: @CZHU20 (Chi Zhu)
Repository: https://github.com/SimVascular/svFSI
Branch with paper.md (empty if default branch):
Version: 2022.09.26
Editor: @Kevin-Mattheus-Moerman
Reviewers: @chennachaos, @JaroslavHron, @axel-loewe
Archive: 10.5281/zenodo.7113485

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83"><img src="https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83/status.svg)](https://joss.theoj.org/papers/cf1aa78cd6e9d4cbf818053aef61bc83)

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

@chennachaos & @JaroslavHron & @ @axel-loewe, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman 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 ✨

Review checklist for @JaroslavHron

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@CZHU20) 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

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 and who the target audience is?
• 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?

Review checklist for @axel-loewe

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@CZHU20) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @chennachaos, @JaroslavHron, @ @axel-loewe it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1210

[whedon]

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1016/j.jelectrocard.2003.09.017 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

PDF failed to compile for issue #4118 with the following error:

 [WARNING] Citeproc: citation axel-loewe not found
Error producing PDF.
! Undefined control sequence.
\hyper@@link ->\let \Hy@reserved@a 
                                   \relax \@ifnextchar [{\hyper@link@ }{\hyp...
l.356 }

Looks like we failed to compile the PDF

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.70 s (107.1 files/s, 46964.6 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
Fortran 77                              79           6159           7485          37515
C                                      121           8078           7418          32300
C++                                      5           3117           6762          27459
C/C++ Header                            50           2780           4050          12528
Fortran 90                               5           1081            353           6067
make                                    46            419            585           2621
CMake                                   35            436            928           2118
Bourne Shell                            35            255            260            680
Markdown                                 5            237              0            680
CSS                                      1             92             47            217
TeX                                      1             16              0            160
Tcl/Tk                                   3             50            110            150
Bourne Again Shell                       7             66             90            142
Windows Module Definition                1              1              6             53
WiX source                               1             10              0             23
HTML                                     1              0              0             12
---------------------------------------------------------------------------------------
SUM:                                   396          22797          28094         122725
---------------------------------------------------------------------------------------


Statistical information for the repository 'e26e085a5a0b9d4a326f71d9' was
gathered on 2022/02/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chi                              1             6              2            0.00
Vijay Vedula                     7           257            205            0.27
alexkaiser                       1             0          50067           29.37
osmsc                            1        119931              0           70.35

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Chi Zhu                       4          100.0          0.6                0.00
Vijay Vedula                256           99.6          8.3               18.75
osmsc                     69660           58.1          0.0               19.87

[Kevin-Mattheus-Moerman]

@whedon re-invite @axel-loewe as reviewer

[whedon]

OK, the reviewer has been re-invited.

@axel-loewe please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[Kevin-Mattheus-Moerman]

@axel-loewe apologies for the second invite. I had added you initially as @ @axel-loewe by mistake. It should be fixed now.

[Kevin-Mattheus-Moerman]

@chennachaos, @JaroslavHron, @axel-loewe thanks for your help with this review!!!! 🥳 You may now start. Let me know if you have any questions.

[axel-loewe]

@whedon generate pdf

[whedon]

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

[JaroslavHron]

Hi @Kevin-Mattheus-Moerman - it seems that i have missed the invitation, and its now expired - could you reinvite me.

[Kevin-Mattheus-Moerman]

@whedon re-invite @JaroslavHron a reviewer

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[axel-loewe]

Zhu et al. present svFSI, a simulation software for cardiac physiology. It covers multiple cardiac functions (physics): solid mechanics, hemodynamics and apparently cardiac electrophysiology. The effort of developing a software for this challenging coupled problem and making if publicly available is appreciated.

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

While there is no LICENSE file, there is Copyright-Simvasscular.txt which holds a license. Renaming might help to make this information more easily findable. The text seems to be the MIT license, I recommend mentioning this explicitly and also adding this information to the metadate of the GitHub project.

Contribution and authorship: Has the submitting author (@CZHU20) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

From the commit history, this does not seem to be the case (3 minor commits only). I am aware that the public commits may not be representative of the entire history of the project. Please comment on it.

Installation: Does installation proceed as outlined in the documentation?

I did not manage to compile the code with clang 13.0 (Undefined identifiers in METISLib).
Do you see an option to increase compatibility with other compilers or to provide a container? In the current form, I cannot evaluate svFSI's functionality.

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

svFSI is introduced as a multi-physics simulator including electrophysiology, tissue mechanics and blood dynamics. Unfortunately, I could not find any information on electrophysiology in the paper or the documentation (http://simvascular.github.io/docssvFSI.html). As such, I suggest to either document these features or to remove these aspects from the paper.
Later on I found this link at the bottom of the README file: http://simvascular.github.io/docsSimCardio.html#cep-modeling
It's not entirely clear to me how SimCardio relates to svFSI and I strongly recommend to provide a comprehensive overview of all relevant documentation for svFSI at a central place.

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

The website lists them but there is no automated way of installing them. Later on, I discovered more detailed information in the INSTALL-DEPS.md file in the repository. Would be good to sync this information with the web page documentation.
Given the high number of dependencies and very specific versions being referred to in the documentation, I encourage you to consider providing a containerized version.

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

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

As coupling multiple physics is a complex problem and also multiplies the number of user-chosen parameters, types of boundary conditions, pre- and postprocessing steps etc., I assume that svFSI probably provides only a subset of features of established single-physics simulators. I believe it would be important for potential new users to learn about which features are supported.
The brief paper remains rather vagues and does not mention the concrete scope. The documentation I found on the website is a tutorial for setting up a fluid-structure simulation (which I believe will be valuable for new users). However, I could not find a comprehensive user manual. The Documentation folder only contains a Doxygen configuration file.
I feel that a proper user documentation is a prerequisite for svFSI to be really useful beyond the group of developers.

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

Could not find such information. There are no CI pipelines implemented as GitHub actions. Cannot judge on external CI.

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

Could not find such information in the repository or the svFSI part of the SimVascular webpage.

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?

Line 27: Please change the reference to openCARP to this one: https://dx.doi.org/10.1016/j.cmpb.2021.106223

• Is the Readme.md file required? Seems it does not hold relevant information for users/developers and might be confused with README.md. Will also cause trouble on non-case-sensitive file systems.

[JaroslavHron]

@Kevin-Mattheus-Moerman - it seems that there was some typo in the re-invitation and it failed

[danielskatz]

@whedon re-invite @JaroslavHron as reviewer

[whedon]

OK, the reviewer has been re-invited.

@JaroslavHron please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[whedon]

👋 @JaroslavHron, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @chennachaos, please update us on how your review is going (this is an automated reminder).

[Kevin-Mattheus-Moerman]

@editorialbot recommend accept

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[Kevin-Mattheus-Moerman]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK
- 10.48550/ARXIV.2201.03303 is OK
- 10.48550/ARXIV.2207.12460 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.cmpb.2021.106223 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.cmpb.2021.106223' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

[Kevin-Mattheus-Moerman]

@CZHU20 this PR should fix these issues with the DOIs: SimVascular/svFSI#92

[CZHU20]

@Kevin-Mattheus-Moerman this pull request has been merged. Thank you.

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1016/j.cmpb.2021.106223 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK
- 10.48550/ARXIV.2201.03303 is OK
- 10.48550/ARXIV.2207.12460 is OK

MISSING DOIs

- Errored finding suggestions for "The LifeV library: engineering mathematics beyond ...", please try later

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@CZHU20 one more pull request: SimVascular/svFSI#93 to fix that missing DOI

[CZHU20]

@Kevin-Mattheus-Moerman Done.

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1016/j.cmpb.2021.106223 is OK
- 10.48550/arXiv.1710.06596 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK
- 10.48550/ARXIV.2201.03303 is OK
- 10.48550/ARXIV.2207.12460 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.jcp.2015.11.022 is OK
- 10.1161/CIRCRESAHA.110.223610 is OK
- 10.1007/s10439-016-1762-8 is OK
- 10.1115/1.4005694 is OK
- 10.1016/j.cmpb.2021.106223 is OK
- 10.48550/arXiv.1710.06596 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1371/journal.pcbi.1005828 is OK
- 10.1371/journal.pcbi.1009331 is OK
- 10.1016/j.jbiomech.2018.03.034 is OK
- 10.1002/cnm.3351 is OK
- 10.1615/Int.J.UncertaintyQuantification.2020033068 is OK
- 10.1007/s10237-020-01294-8 is OK
- 10.1115/1.4048032 is OK
- 10.48550/ARXIV.2201.03303 is OK
- 10.48550/ARXIV.2207.12460 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3598, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[Kevin-Mattheus-Moerman]

Congratulations @CZHU20 on this publication!!!!

@chennachaos, @JaroslavHron and @axel-loewe thank you so much for your fantastic review efforts!!!!!!

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04118 joss-papers#3599
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04118
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[CZHU20]

Thank you all for your help! @Kevin-Mattheus-Moerman @chennachaos @JaroslavHron @axel-loewe

[editorialbot]

🎉🎉🎉 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.04118/status.svg)](https://doi.org/10.21105/joss.04118)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04118">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04118/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04118/status.svg
   :target: https://doi.org/10.21105/joss.04118

This is how it will look in your documentation:

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss