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@Electronic{comparisonSaldamli,
  Title                    = {PDE extension -- Changes over Levon's extension},
  Author                   = {Jan \v{S}ilar},
  Note                     = {https://openmodelica.org/svn/OpenModelica/trunk/doc/PDEInModelica/doc/comparisonToSaldamli.pdf},

  Owner                    = {janek},
  Timestamp                = {2014.10.02}
}

@InCollection{raey,
  Title                    = {On the Role of Mathematical Abstractions for Scientific Computing},
  Author                   = {Ahlander, Krister and Haveraaen, Magne and Munthe-Kaas, HansZ.},
  Booktitle                = {The Architecture of Scientific Software},
  Publisher                = {Springer US},
  Year                     = {2001},
  Editor                   = {Boisvert, RonaldF. and Tang, PingTakPeter},
  Pages                    = {145-158},
  Series                   = {IFIP -- The International Federation for Information Processing},
  Volume                   = {60},

  Doi                      = {10.1007/978-0-387-35407-1_9},
  ISBN                     = {978-1-4757-6719-3},
  Keywords                 = {Abstraction; coordinate-free numerics; object-oriented modeling; PDE simulation.},
  Language                 = {English},
  Url                      = {http://dx.doi.org/10.1007/978-0-387-35407-1_9}
}

@Article{alastrueyarterial,
  Title                    = {Arterial pulse wave haemodynamics},
  Author                   = {Alastruey, Jordi and Parker, Kim H and Sherwin, Spencer J}
}

@Article{hiflow3,
  Title                    = {HiFlow3--A Flexible and Hardware-Aware Parallel Finite Element Package},
  Author                   = {Anzt, Hartwig and Augustin, Werner and Baumann, Martin and Bockelmann, Hendryk and Gengenbach, Thomas and Hahn, Tobias and Heuveline, Vincent and Ketelaer, Eva and Lukarski, Dimitar and Otzen, Andrea and others},
  Journal                  = {Preprint Series of the Engineering Mathematics and Computing Lab},
  Year                     = {2013},
  Number                   = {06}
}

@Book{Arnez2003,
  Title                    = {Simulations in Biomedicine V: },
  Author                   = {Arnez, Z.M. and Brebbia, C.A. and Solina, F. and Stankovski, V.},
  Publisher                = {WIT Press},
  Year                     = {2003},
  Series                   = {WIT Transactions on Biomedicine and Health},

  ISBN                     = {9781853129650},
  Lccn                     = {2003279424},
  Url                      = {http://books.google.cz/books?id=NZ7CAQAAQBAJ}
}

@Misc{Modelica3.3Spec,
  Title                    = {Modelica Specification, version 3.3},

  Author                   = {Modelica Association},
  HowPublished             = {\\https://www.modelica.org/documents/ModelicaSpec33.pdf},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2014.02.25}
}

@MastersThesis{PDELib,
  Title                    = {Support for Dymola in the Modeling and Simulation of Physical Systems with Distributed Parameters},
  Author                   = {Farid Dshabarow},
  School                   = {Dept. f\"{u}r Computational Science, ETH Z\"{u}rich},
  Year                     = {2007},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.11.06}
}

@Book{fritzson2010principles,
  Title                    = {Principles of Object-Oriented Modeling and Simulation with Modelica 2.1},
  Author                   = {Fritzson, Peter},
  Publisher                = {Wiley-IEEE Press},
  Year                     = {2004}
}

@Article{gao2006stress,
  Title                    = {Stress analysis in a layered aortic arch model under pulsatile blood flow},
  Author                   = {Gao, Feng and Watanabe, Masahiro and Matsuzawa, Teruo and others},
  Journal                  = {Biomed Eng Online},
  Year                     = {2006},
  Number                   = {25},
  Pages                    = {1--11},
  Volume                   = {5}
}

@Article{gosling2003terminology,
  Title                    = {Terminology for describing the elastic behavior of arteries},
  Author                   = {Gosling, Raymond G and Budge, Marc M},
  Journal                  = {Hypertension},
  Year                     = {2003},
  Number                   = {6},
  Pages                    = {1180--1182},
  Volume                   = {41},

  Publisher                = {Am Heart Assoc}
}

@Book{guccione2010computational,
  Title                    = {Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure},
  Author                   = {Guccione, J.M. and Kassab, G. and Ratcliffe, M.},
  Publisher                = {Springer},
  Year                     = {2010},

  ISBN                     = {9781441907301},
  Url                      = {http://books.google.cz/books?id=l1u\_8qMhAx4C}
}

@Article{Horacek,
  Title                    = {Numerical simulation of self-oscillations of human vocal folds with Hertz model of impact forces },
  Author                   = {J. Horacek and P. Sidlof and J.G. Svec},
  Journal                  = {Journal of Fluids and Structures },
  Year                     = {2005},
  Note                     = {Axial-Flow Fluid-Structure Interactions Axial-Flow Fluid-Structure Interactions },
  Number                   = {6},
  Pages                    = {853 - 869},
  Volume                   = {20},

  Doi                      = {http://dx.doi.org/10.1016/j.jfluidstructs.2005.05.003},
  ISSN                     = {0889-9746},
  Keywords                 = {Flow induced vibrations},
  Url                      = {http://www.sciencedirect.com/science/article/pii/S0889974605000642}
}

@Book{de1995ventilation,
  Title                    = {Ventilation Modelling of the Human Lung},
  Author                   = {de Jongh, F.H.C.},
  Publisher                = {Delft University of Technology, Faculty of Aerospace Engineering},
  Year                     = {1995},

  ISBN                     = {9789056230142},
  Url                      = {http://books.google.cz/books?id=E60cAAAACAAJ}
}

@Book{keener2009mathematical,
  Title                    = {Mathematical Physiology},
  Author                   = {Keener, J.P. and Sneyd, J.},
  Publisher                = {Springer},
  Year                     = {2009},
  Series                   = {Interdisciplinary Applied Mathematics},

  ISBN                     = {9780387758466},
  Lccn                     = {98014499},
  Url                      = {http://books.google.cz/books?id=HIkZ3QHbpTQC}
}

@TechReport{MaplePDE,
  Title                    = {Discretizing pdes for maplesim},
  Author                   = {Samir Khan},
  Institution              = {Adept Scientific},
  Year                     = {2012},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.11.06}
}

@Article{kofranek2011hummod,
  Title                    = {Hummod-large scale physiological models in modelica},
  Author                   = {Kofranek, Jiri and Matejak, Marek and Privitzer, Pavol},
  Year                     = {2011},

  Publisher                = {Citeseer}
}

@Article{kofranek2011atlas,
  Title                    = {The Atlas of Physiology and Pathophysiology: Web-based multimedia enabled interactive simulations},
  Author                   = {Kofranek, Jiri and Matousek, Stanislav and Rusz, Jan and Stodulka, Petr and Privitzer, Pavol and Matejak, Marek and Tribula, Martin},
  Journal                  = {Computer methods and programs in biomedicine},
  Year                     = {2011},
  Number                   = {2},
  Pages                    = {143--153},
  Volume                   = {104},

  Publisher                = {Elsevier}
}

@Article{PeripheralArterial,
  Title                    = {Measurement of regional elastic properties of the human aorta. A new application of transesophageal echocardiography with automated border detection and calibrated subclavian pulse tracings.},
  Author                   = {Lang, Roberto M and Cholley, Bernard P and Korcarz, Claudia and Marcus, Richard H and Shroff, Sanjeev G},
  Journal                  = {Circulation},
  Year                     = {1994},
  Number                   = {4},
  Pages                    = {1875--1882},
  Volume                   = {90},

  Publisher                = {Am Heart Assoc}
}

@Article{layton1991bifurcation,
  Title                    = {Bifurcation analysis of TGF-mediated oscillations in SNGFR},
  Author                   = {Layton, HE and Pitman, E BRUCE and Moore, LEON C},
  Journal                  = {Amer. J. Physiol},
  Year                     = {1991},
  Volume                   = {261}
}

@Book{leveque2007finite,
  Title                    = {Finite difference methods for ordinary and partial differential equations: steady-state and time-dependent problems},
  Author                   = {LeVeque, Randall},
  Publisher                = {Society for Industrial and Applied Mathematics},
  Year                     = {2007}
}

@InProceedings{Li2008,
  Title                    = {Solving PDE models in Modelica},
  Author                   = {Li, Zhihua and Zheng, Ling and Zhang, Huili},
  Booktitle                = {Information Science and Engineering, 2008. ISISE'08. International Symposium on Information Science and Engieering. ISISE},
  Year                     = {2008},
  Organization             = {IEEE},
  Pages                    = {53--57},
  Volume                   = {1}
}

@InProceedings{li2008solving,
  Title                    = {Solving PDE Models in Modelica},
  Author                   = {Li, Zhihua and Zheng, Ling and Zhang, Huili},
  Booktitle                = {Proceedings of the 2008 International Symposium on Information Science and Engieering-Volume 01},
  Year                     = {2008},
  Organization             = {IEEE Computer Society},
  Pages                    = {53--57}
}

@Article{martinson2003index,
  Title                    = {Index and characteristic analysis of linear PDAE systems},
  Author                   = {Martinson, Wade S and Barton, Paul I},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {2003},
  Number                   = {3},
  Pages                    = {905--923},
  Volume                   = {24},

  Publisher                = {SIAM}
}

@Article{martinson2000differentiation,
  Title                    = {A differentiation index for partial differential-algebraic equations},
  Author                   = {Martinson, Wade S and Barton, Paul I},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {2000},
  Number                   = {6},
  Pages                    = {2295--2315},
  Volume                   = {21},

  Publisher                = {SIAM}
}

@Book{murray2003mathematical,
  Title                    = {Mathematical Biology II: Spatial Models and Biomedical Applications},
  Author                   = {Murray, J.D.},
  Publisher                = {Springer},
  Year                     = {2003},
  Series                   = {Intercisciplinary Applied Mathematics: Mathematical Biology},

  ISBN                     = {9780387952284},
  Lccn                     = {2001020448},
  Url                      = {http://books.google.cz/books?id=Dk8pFkP2cKYC}
}

@PhdThesis{saldamli2006pdemodelica,
  Title                    = {A High-Level Language for Modeling with Partial Differential Equations},
  Author                   = {Saldamli, Levon},
  School                   = {Department of Computer and Information Science, Link{\"o}ping University},
  Year                     = {2006}
}

@InProceedings{saldamli2005framework,
  Title                    = {A framework for describing and solving PDE models in Modelica},
  Author                   = {Saldamli, Levon and Bachmann, Bernhard and Wiesmann, Hansj{\"u}rg and Fritzson, Peter},
  Booktitle                = {Paper presented at the 4th International Modelica Conference},
  Year                     = {2005}
}

@Book{schiesser1991numerical,
  Title                    = {The numerical method of lines: integration of partial differential equations},
  Author                   = {Schiesser, William E and Schiesser, William E},
  Publisher                = {Academic Press San Diego},
  Year                     = {1991},
  Volume                   = {212}
}

@Article{sherwin2003one,
  Title                    = {One-dimensional modelling of a vascular network in space-time variables},
  Author                   = {Sherwin, SJ and Franke, V and Peir{\'o}, J and Parker, K},
  Journal                  = {Journal of Engineering Mathematics},
  Year                     = {2003},
  Number                   = {3-4},
  Pages                    = {217--250},
  Volume                   = {47},

  Publisher                = {Springer}
}

@Book{sneyd2008mathematical,
  Title                    = {Mathematical physiology},
  Author                   = {Sneyd, James and Keener, James},
  Publisher                = {Springer-Verlag New York},
  Year                     = {2008}
}

@Article{PDEModelingHiFlow3,
  Title                    = {PDE Modeling with Modelica via FMI Import of HiFlow3 C++ Components},
  Author                   = {Kristian Stav{\aa}ker and Staffan Ronn{\aa}s and Martin Wlotzka and Vincent Heuveline and Peter Fritzson},
  Note                     = {Accepted},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.10.14}
}

@Conference{HiFlow3FMI,
  Title                    = {PDE Modeling with Modelica via FMI Import of HiFlow3 C++ Components},
  Author                   = {Kristian Stav{\aa}ker and Stafan Ronn{\aa}s and Martin Wlotzka and Vincent Heuveline and Peter Fritzson},
  Booktitle                = {SIMS 54th conference Bergen University College, Norway},
  Year                     = {2013},
  Month                    = {October},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.11.10}
}

@Misc{KristiansSlides,
  Title                    = {Demonstration: Using HiFlow3 together with Modelica},

  Author                   = {Kristian Stavaker},
  HowPublished             = {Slides},
  Month                    = {March 26},
  Year                     = {2013},

  Owner                    = {janeks},
  Timestamp                = {2013.08.06}
}

@Article{vazquez2011massively,
  Title                    = {A massively parallel computational electrophysiology model of the heart},
  Author                   = {V{\'a}zquez, M and Ar{\'\i}s, R and Houzeaux, G and Aubry, R and Villar, P and Garcia-Barn{\'e}s, J and Gil, D and Carreras, F},
  Journal                  = {International Journal for Numerical Methods in Biomedical Engineering},
  Year                     = {2011},
  Number                   = {12},
  Pages                    = {1911--1929},
  Volume                   = {27},

  Publisher                = {Wiley Online Library}
}

@Article{voelcker1977constructive,
  Title                    = {Constructive solid geometry},
  Author                   = {Voelcker, Herbert and Requicha, Aristides},
  Year                     = {1977}
}

@Article{voges2012normal,
  Title                    = {Normal values of aortic dimensions, distensibility, and pulse wave velocity in children and young adults: a cross-sectional study},
  Author                   = {Voges, Inga and Jerosch-Herold, Michael and Hedderich, J{\"u}rgen and Pardun, Eileen and Hart, Christopher and Gabbert, Dominik Daniel and Hansen, Jan Hinnerk and Petko, Colin and Kramer, Hans-Heiner and Rickers, Carsten and others},
  Journal                  = {Journal of Cardiovascular Magnetic Resonance},
  Year                     = {2012},
  Number                   = {1},
  Pages                    = {77},
  Volume                   = {14},

  Publisher                = {BioMed Central Ltd}
}

@Misc{acoustic,
  Title                    = {Acoustic theory},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Acoustic\_theory},

  Owner                    = {Jan},
  Timestamp                = {2013.09.27}
}

@Misc{advection,
  Title                    = {Advection equation},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Advection},

  Owner                    = {janeks},
  Timestamp                = {2013.06.26}
}

@Misc{blood-viscosity,
  Title                    = {Blood viscosity},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Blood\_viscosity},

  Owner                    = {Jan},
  Timestamp                = {2013.09.20}
}

@Misc{hagen-poiseuille,
  Title                    = {Hagen--Poiseuille equation},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Hagen%E2%80%93Poiseuille_equation},

  Owner                    = {Jan},
  Timestamp                = {2013.09.20}
}

@Misc{HeatEq,
  Title                    = {Heat Equation},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Heat\_equation},

  Owner                    = {janeks},
  Timestamp                = {2013.05.21}
}

@Misc{membrane,
  Title                    = {Vibrating membrane},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Vibrations\_of\_a\_circular\_membrane},

  Owner                    = {Jan},
  Timestamp                = {2013.09.27}
}

@Misc{prestupTepla,
  Title                    = {Přestup tepla},

  Author                   = {Wikipedia},
  Note                     = {http://cs.wikipedia.org/wiki/Přestup\_tepla},

  Owner                    = {janeks},
  Timestamp                = {2013.05.21}
}

@Misc{SolidModeling,
  Title                    = {Solid Modeling},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Solid\_modeling},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.11.05}
}

@Misc{string,
  Title                    = {Vibrating string},

  Author                   = {Wikipedia},
  Note                     = {http://en.wikipedia.org/wiki/Vibrating\_string},

  Owner                    = {janeks},
  Timestamp                = {2013.06.26}
}

@Electronic{FMIWeb,
  Title                    = {The Functional Mockup Interface (FMI)},
  Note                     = {https://www.fmi-standard.org/},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.11.10}
}

@Electronic{Modelica,
  Title                    = {Modelica Association},
  Note                     = {http://www.modelica.org},

  Owner                    = {janek},
  Quality                  = {1},
  Timestamp                = {2013.11.10}
}

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