[PRE REVIEW]: VaMPy: An Automated and Objective Pipeline for Modeling Vascular Geometries

[editorialbot]

Submitting author: !--author-handle-->@hkjeldsberg<!--end-author-handle-- (Henrik Aasen Kjeldsberg) Repository: https://github.com/KVSlab/VaMPy Branch with paper.md (empty if default branch): joss-paper Version: v1.0.1 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @stefsmeets, @JaroslavHron, @ctdegroot Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6392e1591375274eec66eddf845a31f3"><img src="https://joss.theoj.org/papers/6392e1591375274eec66eddf845a31f3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6392e1591375274eec66eddf845a31f3/status.svg)](https://joss.theoj.org/papers/6392e1591375274eec66eddf845a31f3)

Author instructions

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

@hkjeldsberg 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=0.09 s (728.0 files/s, 97686.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          28           1073           1035           3620
Markdown                        18            268              0            914
TeX                              2             58             28            576
C++                              3             32             46            377
YAML                             6             62             30            247
C/C++ Header                     2             61             27             75
XML                              1              0              0             51
TOML                             1              5              2             47
Bourne Shell                     1             16             32             24
Dockerfile                       1              9              5             14
JSON                             1              0              0              8
reStructuredText                 1             28             72              8
make                             1              2              0              4
-------------------------------------------------------------------------------
SUM:                            66           1614           1277           5965
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1291

[Kevin-Mattheus-Moerman]

@editorialbot assign me as editor

[editorialbot]

Assigned! @Kevin-Mattheus-Moerman is now the editor

[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

- 10.1016/j.jfluidstructs.2005.04.006 is OK
- 10.1152/japplphysiol.00118.2008 is OK

MISSING DOIs

- 10.3174/ajnr.a3793 may be a valid DOI for title: Mind the gap: impact of computational fluid dynamics solution strategy on prediction of intracranial aneurysm hemodynamics and rupture status indicators
- 10.3174/ajnr.a4263 may be a valid DOI for title: Narrowing the expertise gap for predicting intracranial aneurysm hemodynamics: impact of solver numerics versus mesh and time-step resolution
- 10.1016/j.jbiomech.2014.04.018 may be a valid DOI for title: High-resolution computational fluid dynamics detects flow instabilities in the carotid siphon: implications for aneurysm initiation and rupture?
- 10.1007/s10439-015-1525-y may be a valid DOI for title: Transitional flow in the venous side of patient-specific arteriovenous fistulae for hemodialysis
- 10.1016/0045-7825(92)90042-i may be a valid DOI for title: Computational methods in Lagrangian and Eulerian hydrocodes
- 10.1016/0021-9991(84)90125-6 may be a valid DOI for title: Conservative rezoning (remapping) for general quadrilateral meshes
- 10.1016/s0021-9991(02)00033-5 may be a valid DOI for title: Second-order sign-preserving conservative interpolation (remapping) on general grids
- 10.1016/j.jcp.2011.05.003 may be a valid DOI for title: Two-step hybrid conservative remapping for multimaterial arbitrary Lagrangian-Eulerian methods
- 10.1016/j.jcp.2011.12.033 may be a valid DOI for title: One-step hybrid remapping algorithm for multi-material arbitrary Lagrangian-Eulerian methods
- 10.21105/joss.02089 may be a valid DOI for title: turtleFSI: A robust and monolithic FEniCS-based fluid-structure interaction solver
- 10.1002/fld.3996 may be a valid DOI for title: A swept intersection-based remapping method for axisymmetric ReALE computation
- 10.1007/978-3-642-58535-7_5 may be a valid DOI for title: Numerical methods for gasdynamic systems on unstructured meshes
- 10.1016/j.jcp.2009.10.039 may be a valid DOI for title: Optimization-based synchronized flux-corrected conservative interpolation (remapping) of mass and momentum for arbitrary Lagrangian-Eulerian methods
- 10.1016/s0021-9991(03)00187-6 may be a valid DOI for title: An efficient linearity-and-bound-preserving remapping method
- 10.1016/j.jcp.2011.06.030 may be a valid DOI for title: On simplifying ‘incremental remap’-based transport schemes
- 10.4208/cicp.oa-2015-0021 may be a valid DOI for title: Local error analysis and comparison of the swept- and intersection-based remapping methods
- 10.1006/jcph.2000.6465 may be a valid DOI for title: Incremental remapping as a transport/advection algorithm
- 10.1007/978-3-642-20671-9_66 may be a valid DOI for title: Flux-based approach for conservative remap of multi-material quantities in 2D arbitrary Lagrangian-Eulerian simulations
- 10.1016/j.jcp.2005.03.019 may be a valid DOI for title: A subcell remapping method on staggered polygonal grids for arbitrary-Lagrangian-Eulerian methods
- 10.2514/6.2003-3986 may be a valid DOI for title: Revisiting the least-squares procedure for gradient reconstruction on unstructured meshes
- 10.1016/j.cma.2007.10.002 may be a valid DOI for title: Multi-scale Lagrangian shock hydrodynamics on Q1/P0 finite elements: Theoretical framework and two-dimensional computations
- 10.1006/jcph.1998.5952 may be a valid DOI for title: Elimination of artificial grid distortion and hourglass-type motions by means of Lagrangian subzonal masses and pressures
- 10.1007/s003660050021 may be a valid DOI for title: Winslow smoothing on two-dimensional unstructured meshes
- 10.1098/rspa.1937.0036 may be a valid DOI for title: Mechanism of the production of small eddies from large ones
- 10.1002/cnm.3150 may be a valid DOI for title: The FDA nozzle benchmark: ’In theory there is no difference between theory and practice, but in practice there is’
- 10.1007/s10494-018-9905-7 may be a valid DOI for title: Direct numerical simulation of laminar-turbulent transition in a non-axisymmetric stenosis model for newtonian vs. shear-thinning non-newtonian rheologies
- 10.1007/s10439-010-9901-0 may be a valid DOI for title: Image-based modeling of blood flow and vessel wall dynamics: applications, methods and future directions
- 10.1016/j.jbiomech.2008.03.038 may be a valid DOI for title: Direct numerical simulation of transitional flow in a stenosed carotid bifurcation
- 10.1093/acprof:oso/9780198528692.001.0001 may be a valid DOI for title: Spectral/hp Element Methods for Computational Fluid Dynamics
- 10.1016/0045-7825(94)90042-6 may be a valid DOI for title: Unconditional stability and long-term behavior of transient algorithms for the incompressible Navier-Stokes and Euler equations
- 10.1088/0967-3334/31/3/002 may be a valid DOI for title: Characterization of volumetric flow rate waveforms at the carotid bifurcations of older adults
- 10.1007/s10439-015-1288-5 may be a valid DOI for title: Estimation of inlet flow rates for image-based aneurysm CFD models: where and how to begin?
- 10.1016/j.jbiomech.2016.12.004 may be a valid DOI for title: Improved reduced-order modelling of cerebrovascular flow distribution by accounting for arterial bifurcation pressure drops
- 10.1016/j.jbiomech.2011.08.015 may be a valid DOI for title: Direct numerical simulation of transitional flow in a patient-specific intracranial aneurysm
- 10.3171/2019.4.focus19123 may be a valid DOI for title: How patient specific are patient-specific computational models of cerebral aneurysms? An overview of sources of error and variability
- 10.21105/joss.01065 may be a valid DOI for title: morphMan: Automated manipulation of vascular geometries

INVALID DOIs

- None

[hkjeldsberg]

@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:

[hkjeldsberg]

@editorialbot commands

[editorialbot]

Hello @hkjeldsberg, 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

[hkjeldsberg]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.3174/ajnr.a3793 is OK
- 10.3174/ajnr.a4263 is OK
- 10.1016/j.jbiomech.2014.04.018 is OK
- 10.1002/cnm.3150 is OK
- 10.1007/s10494-018-9905-7 is OK
- 10.1007/s10439-010-9901-0 is OK
- 10.1115/1.4023382 is OK
- 10.1007/s13239-018-00374-2 is OK
- 10.1016/j.jacc.2012.11.083 is OK
- 10.1016/j.jfluidstructs.2005.04.006 is OK
- 10.1016/j.jbiomech.2008.03.038 is OK
- 10.1016/j.cpc.2014.10.026 is OK
- 10.1093/acprof:oso/9780198528692.001.0001 is OK
- 10.1088/0967-3334/31/3/002 is OK
- 10.1007/s10439-015-1288-5 is OK
- 10.1016/j.jbiomech.2016.12.004 is OK
- 10.1016/j.jbiomech.2011.08.015 is OK
- 10.3171/2019.4.focus19123 is OK
- 10.21105/joss.01065 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[hkjeldsberg]

Hi @Kevin-Mattheus-Moerman,

We would like to suggest reaching out to @brainstorm and @rlizzo to review our paper since they have reviewed a similar paper in JOSS, which VaMPY builds upon.

Additionally, we believe that @JaroslavHron, @ctdegroot, @capitalaslash, and herbert.owen@bsc.es would be ideal candidates for reviewing this software/paper, given their expertise in CFD and/or FEM.

[Kevin-Mattheus-Moerman]

@hkjeldsberg thanks for suggesting those reviewers. In the future, and if you have more reviewers to suggest, please leave out the @ symbol so they are not tagged yet.

[Kevin-Mattheus-Moerman]

@brainstorm @rlizzo @ElenaFagg @JaroslavHron, @ctdegroot, @capitalaslash @wouterpotters @aslakbergersen @ktbolt @thewtex @vijaysm @stefsmeets @prashjha would you be interested in reviewing this work for JOSS? The paper title is "VaMPy: An Automated and Objective Pipeline for Modeling Vascular Geometries", and it concerns a Python library for vascular modelling. As you might know, reviewing for JOSS means you evaluate/review the software and review a short paper. Links are given below. Let me know if you are interested. Thanks!

Software: https://github.com/KVSlab/VaMPy Paper: https://raw.githubusercontent.com/openjournals/joss-papers/joss.05235/joss.05235/10.21105.joss.05235.pdf Information about reviewing for JOSS: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[stefsmeets]

Hi @Kevin-Mattheus-Moerman I would be happy to review this submission. I have 2-3 busy weeks coming up, but I will have time afterwards.

[Kevin-Mattheus-Moerman]

@stefsmeets that sounds fine. Thanks for the help!

[Kevin-Mattheus-Moerman]

@editorialbot add @stefsmeets as reviewer

[editorialbot]

@stefsmeets added to the reviewers list!

[vijaysm]

Yes, I should have time to review this month.

[JaroslavHron]

Hi, I will be glad to review this contribution. Jaroslav Hron

On March 9, 2023 11:08:05 AM GMT+01:00, Kevin Mattheus Moerman @.***> wrote:

@brainstorm @rlizzo @ElenaFagg @JaroslavHron, @ctdegroot, @capitalaslash @wouterpotters @aslakbergersen @ktbolt @thewtex @vijaysm @stefsmeets @prashjha would you be interested in reviewing this work for JOSS? The paper title is "VaMPy: An Automated and Objective Pipeline for Modeling Vascular Geometries", and it concerns a Python library for vascular modelling. As you might know, reviewing for JOSS means you evaluate/review the software and review a short paper. Links are given below. Let me know if you are interested. Thanks!

Software: https://github.com/KVSlab/VaMPy Paper: https://raw.githubusercontent.com/openjournals/joss-papers/joss.05235/joss.05235/10.21105.joss.05235.pdf Information about reviewing for JOSS: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

-- Reply to this email directly or view it on GitHub: https://github.com/openjournals/joss-reviews/issues/5235#issuecomment-1461717338 You are receiving this because you were mentioned.

Message ID: @.***> -- Sent from my Android device with K-9 Mail. Please excuse my brevity.

[ctdegroot]

I am willing to review as well. I may not have time in the next 2 weeks, but I can complete it soon after.

[Kevin-Mattheus-Moerman]

@editorialbot add @JaroslavHron as reviewer

[editorialbot]

@JaroslavHron added to the reviewers list!

[Kevin-Mattheus-Moerman]

@editorialbot add @ctdegroot as reviewer

[editorialbot]

@ctdegroot added to the reviewers list!

[Kevin-Mattheus-Moerman]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5278.