JOSS review: Fix DOIs (#174)

Co-authored-by: menon-karthik <[email protected]>

Author: menon-karthik

paper/paper.bib

@@ -7,6 +7,7 @@ @article{JANSEN2000305
 year = {2000},
 issn = {0045-7825},
 url = {https://doi.org/10.1016/S0045-7825(00)00203-6},
+doi = {10.1016/S0045-7825(00)00203-6},
 author = {Kenneth E. Jansen and Christian H. Whiting and Gregory M. Hulbert},
 }
 
@@ -70,6 +71,7 @@ @Book{bazilevs13
   owner            = {pfaller},
   pagetotal        = {406},
   url              = {https://onlinelibrary.wiley.com/doi/book/10.1002/9781118483565},
+  doi              = {10.1002/9781118483565},
 }
 
 @article{pfaller2019importance,
@@ -90,7 +92,8 @@ @article{menon2023predictors
   volume={16},
   pages={1099--1109},
   year={2023},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1007/s12265-023-10374-w},
 }
 
 @article{sankaran2012patient,
@@ -136,17 +139,15 @@ @article{menon2024personalized
   year = {2024}
 }
 @article{richter2024bayesian,
-  title={Bayesian Windkessel calibration using optimized 0D surrogate models}, 
-  author={Jakob Richter and Jonas Nitzler and Luca Pegolotti and Karthik Menon and Jonas Biehler and Wolfgang A. Wall and Daniele E. Schiavazzi and Alison L. Marsden and Martin R. Pfaller},
-  year={2024},
-  volume={2404.14187},
-  journal={arXiv},
-}
-@MISC{eigenweb,
-  author = {Ga\"{e}l Guennebaud and Beno\^{i}t Jacob and others},
-  title = {Eigen v3},
-  howpublished = {http://eigen.tuxfamily.org},
-  year = {2010}
+  title={Bayesian Windkessel calibration using optimized zero-dimensional surrogate models},
+  author={Richter, Jakob and Nitzler, Jonas and Pegolotti, Luca and Menon, Karthik and Biehler, Jonas and Wall, Wolfgang A and Schiavazzi, Daniele E and Marsden, Alison L and Pfaller, Martin R},
+  journal={Philosophical Transactions A},
+  volume={383},
+  number={2292},
+  pages={20240223},
+  year={2025},
+  publisher={The Royal Society},
+  doi={10.1098/rsta.2024.0223}
 }
 
 @article{Kim2009,
@@ -298,6 +299,7 @@ @article{menon2024personalizeduncertainty
       volume={2409.02247},
       journal={arXiv},
       url={https://arxiv.org/abs/2409.02247},
+      doi={10.48550/arXiv.2409.02247}
 }
 
 @article{AFRICA2024109039,
@@ -347,7 +349,7 @@ @article{REGAZZONI2021104641
 pages = {104641},
 year = {2021},
 issn = {0010-4825},
-doi = {https://doi.org/10.1016/j.compbiomed.2021.104641},
+doi = {10.1016/j.compbiomed.2021.104641},
 url = {https://www.sciencedirect.com/science/article/pii/S0010482521004352},
 author = {F. Regazzoni and A. Quarteroni},
 keywords = {Mathematical modeling, Cardiac modeling, Cardiac electromechanics, Multiphysics models, Lumped-parameter models}
@@ -361,7 +363,8 @@ @article{benemerito2024openbf
   number={12},
   pages={125002},
   year={2024},
-  publisher={IOP Publishing}
+  publisher={IOP Publishing},
+  doi={10.1088/1361-6579/ad9663}
 }
 
 @article{cellml,
@@ -372,7 +375,7 @@ @article{cellml
 volume = {17},
 number = {2-3},
 journal = {Journal of Integrative Bioinformatics},
-doi = {doi:10.1515/jib-2020-0021},
+doi = {10.1515/jib-2020-0021},
 year = {2020}
 }
 
@@ -384,6 +387,16 @@ @inproceedings{alastruey2012arterial
   year={2012},
   organization={Virtual PiE Led t/a BHR Group}
 }
+@article{alastruey2012arterial,
+  title={Physical determining factors of the arterial pulse waveform: theoretical analysis and calculation using the 1-D formulation},
+  author={Alastruey, Jordi and Passerini, Tiziano and Formaggia, Luca and Peir{\'o}, Joaquim},
+  journal={Journal of Engineering Mathematics},
+  volume={77},
+  pages={19--37},
+  year={2012},
+  publisher={Springer},
+  doi={10.1007/s10665-012-9555-z}
+}
 
 @article{heldt2010cvsim,
   title={CVSim: an open-source cardiovascular simulator for teaching and research},
@@ -401,7 +414,7 @@ @article{HUTTARY2017104
 pages = {104-123},
 year = {2017},
 issn = {0010-4825},
-doi = {https://doi.org/10.1016/j.compbiomed.2017.05.021},
+doi = {10.1016/j.compbiomed.2017.05.021},
 url = {https://www.sciencedirect.com/science/article/pii/S0010482517301439},
 author = {Rudolf Huttary and Leonid Goubergrits and Christof Schütte and Stefan Bernhard},
 keywords = {Windkessel elements, Lumped models, 0D modeling, Multi-compartment modeling, Cardiovascular simulation, Distributed parameter modeling, Clinical data set, Coarctation of aorta, Patient-specific models, Disease-specific models, Multiscale modeling}
@@ -415,5 +428,6 @@ @article{rosalia2021object
   number={3},
   pages={2000216},
   year={2021},
-  publisher={Wiley Online Library}
+  publisher={Wiley Online Library},
+  doi={10.1002/adts.202000216}
 }

paper/paper.md

@@ -124,7 +124,7 @@ The zero-dimensional simulations performed by `svZeroDSolver` are governed by no
 We integrate these equations in time using the implicit generalized-alpha scheme [@JANSEN2000305] with Newton-Raphson iterations to solve the linearized system.
 Under the hood, these linearized governing equations for each block are implemented as local contributions to a system of linear (matrix) equations, which are then assembled into a global linear system based on the user-specified configuration.
 Details on the modular implementation of the blocks, along with their governing equations, are provided in the documentation's [Developer Guide](https://simvascular.github.io/svZeroDSolver/developer_guide.html).
-We use the [Eigen package](https://gitlab.com/libeigen/eigen) to represent and solve these sparse linear systems [@eigenweb].
+We use the [Eigen package](https://gitlab.com/libeigen/eigen) to represent and solve these sparse linear systems.
 Mathematical details on this implementation are provided in the [`SparseSystem`](https://simvascular.github.io/svZeroDSolver/class_sparse_system.html#details) and [`Integrator`](https://simvascular.github.io/svZeroDSolver/class_integrator.html#details) classes in the documentation.
 
 `svZeroDSolver` currently has implementations of different types of blood vessel blocks with non-linear resistors to model vascular stenoses, junctions between blood vessels, a heart valve block modeled using a hyperbolic tangent function, a cardiac chamber block modeled as a time-varying capacitor and inductor, and several boundary condition blocks including simple flow, pressure and resistors blocks, windkessel boundary conditions, coronary boundary conditions that include the intramyocardial pressure experienced by coronary arteries, as well as two-sided versions of windkessel and coronary boundary conditions that allow a user to build closed-loop circulation models [@Vignon-Clementel2006; @Kim2009; @kimcoronary; @Mirramezani2019; @menon2023predictors; @menon2024personalized].