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                                       GENERAL
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Contains the key materials required for reproducibility of the DPhil thesis (2024)

"Investigations of electrophysiological mechanisms related to myocardial ischaemia in
hypertrophic cardiomyopathy: implications for arrhythmic risk, ECG diagnosis, and
antiarrhythmic therapy"

Contact: james.alec.coleman@gmail.com

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Subfolders corresponding to Chapters 6 - 8 contain the relevant meshes, config file
templates, and modified MonoAlg3D sources. Modifications were typically made in the
following src libraries:

models_library/ToROrd; domains_library; extra_data_library; monodomain

Of note, MonoAlg3D was updated by Rafael Sachetto over the course of the thesis, to
include ECG computation, ensight save formats, and changes to allow fibrosis to be 
modelled as non-conducting elements.

MonoAlg3D may require further adaptation for the specific HPC in use.

In versions enabled for investigations of populations of action potential models,
directories must be changed to load the population conductance multipliers and initial
state vectors, which were loaded from .npy files using the cnpy.h header.

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                                       CREDIT
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Septal and Apical HCM biventricular meshes were adapted from previous work by Lyon et
al. 2018 (doi: 10.1093/europace/euy226)

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The ToR-ORd action potential model is attributed to Tomek et al. 2019 
(doi: 10.7554/eLife.48890)

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The ionic remodelling pattern used in HCM cells is attributed to Passini et al. 2016
(doi: 10.1016/j.yjmcc.2015.09.003)

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The original MonoAlg3D source from Rafael Sachetto was adapted under MIT license
(https://github.com/rsachetto/MonoAlg3D_C), requiring the following permission notice:

Copyright (c) 2017 Rafael Sachetto

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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The C header file used to load .npy files ("cnpy.h") from Carl Rogers was adapted 
under MIT license (https://github.com/rogersce/cnpy), requiring the following 
permission notice:

Copyright (c) Carl Rogers, 2011

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

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