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FIx link to demo notebooks and documentation #241

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May 21, 2021
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FIx link to demo notebooks and documentation #241

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4 changes: 2 additions & 2 deletions paper.md
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Expand Up @@ -53,7 +53,7 @@ Changes in cell neighbours - also called rearangements - happen when the size of

Cell elimination happens when a cell area (volume) reaches a low threshold. When this happens, cell starts to loose contact with neighboring cells through series of rearangements. Once the cell is reduced to a triangle (in 2D) or a tetrahedron (in 3D) the remaining vertices are merged to create a new vertex.

Although it was customary to assume the neighbor exchange to be a single step process, we follow the work by Finegan et al. which describes cell exchange as a multistep, stochastic process [@Finegan:2019]. As a consequence, in `tyssue`, vertices are not limited to 3 (in 2D) or 4 (in 3D) linked edges, but can form "rosettes" - see [type1](https://github.com/DamCB/tyssue-demo/blob/master/06-Type_1_transition.ipynb) and [rosette](https://github.com/DamCB/tyssue-demo/blob/master/08-Rosettes.ipynb) examples.
Although it was customary to assume the neighbor exchange to be a single step process, we follow the work by Finegan et al. which describes cell exchange as a multistep, stochastic process [@Finegan:2019]. As a consequence, in `tyssue`, vertices are not limited to 3 (in 2D) or 4 (in 3D) linked edges, but can form "rosettes" - see [type1 and rosette](https://github.com/DamCB/tyssue-demo/blob/master/05-Rearangments.ipynb) examples.


### Mechanics
Expand All @@ -74,7 +74,7 @@ This way, it is easy to test various combinations of energy terms and find those
**Figure 2: Organisation of different part of tyssue**


Documentation of the `tyssue` Python library can be found [here](https://tyssue.readthedocs.io/en/latest/). Notebook introduction to how to use `tyssue` library can be found [here](https://github.com/DamCB/tyssue-demo).
Documentation of the `tyssue` Python library can be found [here](http://tyssue.io/). Notebook introduction to how to use `tyssue` library can be found [here](https://github.com/DamCB/tyssue-demo).

The `tyssue` library has already been used in several studies with different context of epithelia morphogenesis, such as leg folding and mesoderm invagination in *Drosophila melanogaster* ([@Monier:2015], [@Gracia:2019], [@Martin:2021]). Github repository from those publications can be found [here](https://github.com/glyg/leg-joint), [here](https://github.com/suzannelab/invagination) and [here](https://github.com/suzannelab/polarity) respectively.

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