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Small fixes in the JOSS paper
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ankushaggarwal committed Jan 23, 2025
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Expand Up @@ -121,8 +121,8 @@ In principle, the problems that can be solved using `pyMechT` can also be solved

- The reference zero-stress state of biological tissues can be unknown or ambiguous. Moreover, the biological tissues are heterogeneous, with multiple layers each of varying properties. These aspects are non-trivial to incorporate in a finite element simulation, due to the need for recreating the geometry and/or incompatability of the initial state. However, it is straightforward to simulate these in `pyMechT`.

Overall, there are alternative tools that can perform constitutive model fitting. Commercial finite element software such as [Abaqus](https://www.3ds.com/products/simulia/abaqus) and [Ansys](https://www.ansys.com/) have in-built constitutive model fitting tools. For example, [PolyUMod](https://www.ansys.com/products/structures/polyumod) and [MCalibration](https://www.ansys.com/products/structures/mcalibration). [Hyperfit](https://www.hyperfit.cz/home.php) is a commercial software specifically for constitutive model fitting, with the advantage of having a graphical user interface.
However, these are not free/open-source. There are also open-source tools for constitutive model fitting, such as [matmodelfit](https://github.com/KnutAM/matmodfit/tree/master) and (hyperelastic)[https://github.com/adtzlr/hyperelastic]. However, these are not specifically focussed on tissues and lack the capability of handling layered samples or inflation-extension experiment on tubular structures, common in tissue mechanics. Lastly, most of the existing tools do not incorporate Bayesian inference.
Overall, there are many other tools that can perform constitutive model fitting. Commercial finite element software [Abaqus](https://www.3ds.com/products/simulia/abaqus) and [Ansys](https://www.ansys.com/) have in-built constitutive model fitting tools, such as, [PolyUMod](https://www.ansys.com/products/structures/polyumod) and [MCalibration](https://www.ansys.com/products/structures/mcalibration). [Hyperfit](https://www.hyperfit.cz/home.php) is a commercial software specifically for constitutive model fitting, with the advantage of having a graphical user interface.
However, these are commercial and are not free/open-source. There are alternative open-source tools for constitutive model fitting, such as [matmodelfit](https://github.com/KnutAM/matmodfit/tree/master) and [hyperelastic](https://github.com/adtzlr/hyperelastic). However, these are not specifically focussed on tissues and lack the capability of handling layered samples or inflation-extension experiment on tubular structures, common in tissue mechanics. Lastly, most of the existing tools do not incorporate Bayesian inference, which is important for providing a confidence interval on fitted parameters and model predictions.

# Uses in literature
`pyMechT` has been used for Bayesian model selection based on extensive planar biaxial extension data [@AGGARWAL2023105657]. This work required rapid simulation of varied constitutive models, which was facilitated by `pyMechT`. Similarly, the Bayesian inference via Markov Chain Monte Carlo in `pyMechT` was used to infer the distribution of aortic biomechanical and geometrical properties based on in-vivo measurements (as likelihood) and ex-vivo biaxial extension data (as prior distribution) [@Aggarwal2025]. Moreover, data-driven model developed in @AGGARWAL2023115812 has been used in `pyMechT` via the `splineI1` and `splineI1I4` material models.
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