[PRE REVIEW]: CirculationSystemModels.jl - A ModelingToolkit Library for 0D-Lumped-Parameter Models of the Cardiovascular Circulation

[editorialbot]

Submitting author: !--author-handle-->@TS-CUBED<!--end-author-handle-- (Torsten Schenkel) Repository: https://github.com/TS-CUBED/CirculatorySystemModels.jl Branch with paper.md (empty if default branch): JOSS-Paper Version: v0.1.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c1206ebeed69fc47f477fe3e89254daf"><img src="https://joss.theoj.org/papers/c1206ebeed69fc47f477fe3e89254daf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c1206ebeed69fc47f477fe3e89254daf/status.svg)](https://joss.theoj.org/papers/c1206ebeed69fc47f477fe3e89254daf)

Author instructions

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

@TS-CUBED 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:

@editorialbot commands

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (439.9 files/s, 115281.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                 2              0            107           1298
Julia                            5            536            330           1234
Markdown                         5            156              0            591
TeX                              1              2              1            504
TOML                             3             29              1            101
YAML                             3              0              2             87
-------------------------------------------------------------------------------
SUM:                            19            723            441           3815
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1004

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.21105/joss.04561 is OK
- 10.1080/03091902.2019.1576792 is OK

MISSING DOIs

- 10.1177/0037549703040939 may be a valid DOI for title: An overview of CellML 1.1, a biological model description language
- 10.1016/j.pbiomolbio.2004.01.004 may be a valid DOI for title: CellML: its future, present and past
- Errored finding suggestions for "Circulation: overall regulation", please try later
- 10.1109/iembs.2007.4353539 may be a valid DOI for title: Parameter identifiability of cardiac ionic models using a novel CellML least squares optimization tool
- 10.1007/s10439-014-1234-y may be a valid DOI for title: pyNS: an open-source framework for 0D haemodynamic modelling
- 10.1016/j.pbiomolbio.2015.12.008 may be a valid DOI for title: Myokit: a simple interface to cardiac cellular electrophysiology
- 10.1007/s10558-007-9030-z may be a valid DOI for title: Cardiovascular simulation toolbox
- 10.1109/iscas.2013.6572238 may be a valid DOI for title: An Updated Cardiovascular Simulation Toolbox
- 10.1002/adts.202000216 may be a valid DOI for title: Object-Oriented Lumped-Parameter Modeling of the Cardiovascular System for Physiological and Pathophysiological Conditions
- 10.1080/03091902.2022.2026500 may be a valid DOI for title: OpenModelica-based virtual simulator for the cardiovascular and respiratory physiology of a neonate
- 10.3384/ecp15118459 may be a valid DOI for title: Simulation of large-scale models in modelica: State of the art and future perspectives
- 10.3384/ecp110631 may be a valid DOI for title: Simulation-based development of automotive control software with Modelica
- 10.1016/j.ifacol.2015.05.213 may be a valid DOI for title: Physiolibrary 2.3-An Intuitive Tool for Integrative Physiology
- 10.1109/embc.2015.7318646 may be a valid DOI for title: Physiomodel-an integrative physiology in Modelica
- 10.3384/ecp11063713 may be a valid DOI for title: Hummod-large scale physiological models in modelica
- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1016/j.advengsoft.2022.103173 may be a valid DOI for title: EndoBeams. jl: A Julia finite element package for beam-to-surface contact problems in cardiovascular mechanics
- 10.1088/1742-6596/2090/1/012155 may be a valid DOI for title: Hybrid modeling of the human cardiovascular system using NeuralFMUs
- 10.3390/electronics11111772 may be a valid DOI for title: A Modular, Extensible, and Modelica-Standard-Compliant OpenModelica Compiler Framework in Julia Supporting Structural Variability
- 10.1007/s13239-022-00611-9 may be a valid DOI for title: Patient-Specific Modelling and Parameter Optimisation to Simulate Dilated Cardiomyopathy in Children
- 10.1007/s12265-018-9787-z may be a valid DOI for title: Clinical applications of patient-specific models: The case for a simple approach
- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1152/ajpheart.1996.270.6.h2050 may be a valid DOI for title: Determinants of stroke volume and systolic and diastolic aortic pressure
- 10.1016/j.jbiomech.2005.06.016 may be a valid DOI for title: Numerical simulation of cardiovascular dynamics with healthy and diseased heart valves
- 10.1016/j.medengphy.2003.10.001 may be a valid DOI for title: Minimal haemodynamic system model including ventricular interaction and valve dynamics
- 10.1111/j.1365-2044.1976.tb11804.x may be a valid DOI for title: Poiseuille and his law
- 10.1186/1475-925x-10-33 may be a valid DOI for title: Review of zero-D and 1-D models of blood flow in the cardiovascular system
- 10.1002/cnm.1466 may be a valid DOI for title: A simple, versatile valve model for use in lumped parameter and one-dimensional cardiovascular models
- 10.1016/j.medengphy.2022.103838 may be a valid DOI for title: Dynamic simulation of aortic valve stenosis using a lumped parameter cardiovascular system model with flow regime dependent valve pressure loss characteristics
- 10.1080/03091902.2022.2026500 may be a valid DOI for title: OpenModelica-based virtual simulator for the cardiovascular and respiratory physiology of a neonate
- 10.2139/ssrn.4019246 may be a valid DOI for title: Non-invasive detection of coronary artery disease from photoplethysmograph using lumped parameter modelling
- 10.3384/ecp14096499 may be a valid DOI for title: Physiolibrary-Modelica library for physiology
- 10.1002/adts.202000216 may be a valid DOI for title: Object-Oriented Lumped-Parameter Modeling of the Cardiovascular System for Physiological and Pathophysiological Conditions
- 10.1177/0037549703040939 may be a valid DOI for title: An overview of CellML 1.1, a biological model description language
- Errored finding suggestions for "Modeling and simulation of large-scale systems: A ...", please try later
- 10.3390/electronics11111772 may be a valid DOI for title: A Modular, Extensible, and Modelica-Standard-Compliant OpenModelica Compiler Framework in Julia Supporting Structural Variability
- 10.21203/rs.3.rs-55125/v1 may be a valid DOI for title: Universal differential equations for scientific machine learning

INVALID DOIs

- None

[TS-CUBED]

Hi, thanks for starting the review on our contribution.

We updated paper.bib to include all DOIs but for one reference, which is a github repo without DOI.

Potential reviewers would be:

Chris Rackauckas: ChrisRackauckas Shahriar Iravanian: siravan Ziyi (Francis) Yin: ziyiyin97 Yiannis Simillides : ysimillides

Since the library is built on ModelingToolkit.jl, Chris would be a natural choice, but we would assume him to be super-busy.

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "$end" ($end) [#<BibTeX::Bibliography data=[25]>, "@", #<BibTeX::Entry >, {:title=>["Construction of lumped-parameter cardiovascular models using the {CellML} language"], :volume=>["42"], :url=>["https://doi.org/10.1080/03091902.2019.1576792"], :doi=>["10.1080/03091902.2019.1576792"], :number=>["7"], :journal=>["Journal of Medical Engineering \\& Technology"], :author=>["Shi, Yubing and Lawford, Patricia and Hose, D. Rodney"], :year=>["2018"], :note=>["Publisher: Taylor \\& Francis tex.eprint: https://doi.org/10.1080/03091902.2019.1576792"]}]

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@TS-CUBED thanks for this submission. I have just assigned the query scope label here, which will trigger a scope review by our editorial board. This is normal for submissions that are relatively small in size (e.g. in terms of lines of code). The cope review will check if the work and functionality contained in the submission is substantial enough to warrant publication in JOSS. This scope review should be completed within about 2 weeks.

[TS-CUBED]

https://github.com/TS-CUBED/CirculationModels.jl/commit/dda13a5dd2a40d774c0c9f1701a127890f2aeed3

Added additional Valve Models (Mynard) and fixed error in paper.bib

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/s13239-022-00611-9 is OK
- 10.1007/s12265-018-9787-z is OK
- 10.1137/141000671 is OK
- 10.1152/ajpheart.1996.270.6.H2050 is OK
- 10.1016/j.jbiomech.2005.06.016 is OK
- 10.1016/j.medengphy.2003.10.001 is OK
- 10.1111/j.1365-2044.1976.tb11804.x is OK
- 10.1007/978-1-4419-6363-5 is OK
- 10.1186/1475-925X-10-33 is OK
- 10.1002/cnm.1466 is OK
- 10.1016/j.medengphy.2022.103838 is OK
- 10.1007/s11517-008-0359-2 is OK
- 10.1080/03091902.2022.2026500 is OK
- 10.1016/j.bspc.2022.103781 is OK
- 10.3384/ECP14096499 is OK
- 10.1002/adts.202000216 is OK
- 10.1177/0037549703040939 is OK
- 10.1093/bioinformatics/btg015 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.48550/arXiv.1909.00484 is OK
- 10.3390/electronics11111772 is OK
- 10.21105/joss.04561 is OK
- 10.48550/arXiv.2001.04385 is OK
- 10.5334/jors.151 is OK
- 10.1080/03091902.2019.1576792 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[TS-CUBED]

We have changed the name to CirculatorySystemModels.jl

The original name was too likely to be confused with atmospheric and ocean circulation models.

We have renamed the repo and updated the paper accordingly. Can this be updated, or do we need to resubmit?

[TS-CUBED]

https://github.com/TS-CUBED/CirculatorySystemModels.jl

[Kevin-Mattheus-Moerman]

@editorialbot set https://github.com/TS-CUBED/CirculatorySystemModels.jl as repository

[editorialbot]

Done! repository is now https://github.com/TS-CUBED/CirculatorySystemModels.jl

[TS-CUBED]

Hi, is there anything you need from us at this stage?

[Kevin-Mattheus-Moerman]

@TS-CUBED the scope review by the editorial board has concluded this work is currently not in scope for JOSS. Although the work seems useful and well-coded, the project is a very recent development and appears immature in places. For instance API documentation, the core functionality, and testing, appear limited. We do acknowledge that Julia code is often shorter (in terms of number of lines of code) than some other languages, however, the immaturity of the repository/project, combined with its relatively small size and limited functionality currently cause it to be out of scope. In addition, the README is not detailed enough and community (contributing) guidelines appear missing. Furthermore, the added functionality wrt currently used libraries is not obvious.

We will now proceed to reject this submission. However, since we felt this work was "borderline" in terms of scope, we would invite you the re-submit this work once the authors have addressed the above. In particular we recommend that you consult the review criteria (which refer to testing and community guidelines for instance), while you make these changes too.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.