Update bibliography and figures (DamCB#228)

* Update bibliography

* Update fig + less pixelated images

Author: sophietheis

doc/illus/Figure1.png

@@ -16,6 +16,23 @@ @article{Eritano:2020
 year = {2020}
 }
 
+@article{Cooper:2020,
+author = {Cooper, Fergus and Baker, Ruth and Bernabeu, Miguel and Bordas, Rafel and Bowler, Louise and Bueno-Orovio, Alfonso and Byrne, Helen and Carapella, Valentina and Cardone-Noott, Louie and Cooper, Jonathan and Dutta, Sara and Evans, Benjamin and Fletcher, Alexander and Grogan, James and Guo, Wenxian and Harvey, Daniel and Hendrix, Maurice and Kay, David and Kursawe, Jochen and Maini, Philip and McMillan, Beth and Mirams, Gary and Osborne, James and Pathmanathan, Pras and Pitt-Francis, Joe and Robinson, Martin and Rodriguez, Blanca and Spiteri, Raymond and Gavaghan, David},
+doi = {10.21105/joss.01848},
+issn = {2475-9066},
+journal = {Journal of Open Source Software},
+mendeley-groups = {Modeling},
+month = {mar},
+number = {47},
+pages = {1848},
+publisher = {The Open Journal},
+title = {{Chaste: Cancer, Heart and Soft Tissue Environment}},
+url = {https://joss.theoj.org/papers/10.21105/joss.01848},
+volume = {5},
+year = {2020}
+}
+
+
 @article{Gracia:2019,
 author = {Gracia, M{\'{e}}lanie and Theis, Sophie and Proag, Amsha and Gay, Guillaume and Benassayag, Corinne and Suzanne, Magali},
 doi = {10.1038/s41467-019-10720-0},
@@ -145,25 +162,6 @@ @article{Okuda:2015
 year = {2015}
 }
 
-@article{Mirams:2013,
-author = {Mirams, Gary R. and Arthurs, Christopher J. and Bernabeu, Miguel O. and Bordas, Rafel and Cooper, Jonathan and Corrias, Alberto and Davit, Yohan and Dunn, Sara-Jane and Fletcher, Alexander G. and Harvey, Daniel G. and Marsh, Megan E. and Osborne, James M. and Pathmanathan, Pras and Pitt-Francis, Joe and Southern, James and Zemzemi, Nejib and Gavaghan, David J.},
-doi = {10.1371/journal.pcbi.1002970},
-editor = {Prlic, Andreas},
-issn = {1553-7358},
-journal = {PLoS Computational Biology},
-keywords = {Cardiac electrophysiology,Colorectal cancer,Computational biology,Heart,Open source software,Oxygen,Simulation and modeling,Source code},
-mendeley-groups = {Modeling},
-month = {mar},
-number = {3},
-pages = {e1002970},
-publisher = {Public Library of Science},
-title = {{Chaste: An Open Source C++ Library for Computational Physiology and Biology}},
-url = {https://dx.plos.org/10.1371/journal.pcbi.1002970},
-volume = {9},
-year = {2013}
-}
-
-
 @article{Okuda:2012,
 author = {Okuda, Satoru and Inoue, Yasuhiro and Eiraku, Mototsugu and Sasai, Yoshiki and Adachi, Taiji},
 doi = {10.1007/s10237-012-0430-7},

doc/illus/Figure1.svg

@@ -33,7 +33,7 @@ The `tyssue` Python library seeks to provide a unified interface to implement bi
 # Statement of Need
 <div align="justify">
 
-Tissue remodelling is a complex process integrating a large number of input such as gene expression pattern, cell adherent properties, cell mechanics. It can be difficult to manipulate specific aspects genetically. It can even be hard to simply capture, when the process takes only few minutes. Furthermore, morphogenesis is inherently a mechanical process. To execute complex morphogenetic movements, epithelia are driven by in-plane forces, like constriction of apical cell surface [@Heer:2017], and/or out-of-plane forces, such as the apico-basal cable in apoptotic cell [@Monier:2015, @Gracia:2019] or lateral tension [@Sherrard:2010, @Sui:2018]. Modeling these processes help us understand how tissue acquire their shape, in complement of the experimental systems, and beyond their limitations. Several vertex models have been developed in the past few years to describe the physics of epithelia (for a review, see [@Alt:2017]), and common features can be identified. Several kinds of models have already been published. The apical vertex model has been used several times to study topology changes during morphogenetic movement in _Drosophila, Hydra and Xenopus_([@Staple:2010], [@Farhadifar:2007], [@Aegerter:2012]). Associated with protein dynamics, it has been used to study the effect of protein position on tissue organisation in zebrafish retina ([@Salbreux:2012]). 3D vertex model have been used to study epithelium deformation due to normal development or to cancer development ([@Okuda:2015], [@Eritano:2020]). Most of the time, models are developed for a specific biological question and are difficult to adapt to an other system, for severals reasons. However, there is some exception like Chaste [@Mirams:2013], which propose an open source C++ library to model cell populations or how specific events arise at the system level. With the `tyssue` library, we propose models which are adaptable and scalable with the fied research and the biological question. Topology and mechanics are implement independantly to improve the versatility of models.
+Tissue remodelling is a complex process integrating a large number of input such as gene expression pattern, cell adherent properties, cell mechanics. It can be difficult to manipulate specific aspects genetically. It can even be hard to simply capture, when the process takes only few minutes. Furthermore, morphogenesis is inherently a mechanical process. To execute complex morphogenetic movements, epithelia are driven by in-plane forces, like constriction of apical cell surface [@Heer:2017], and/or out-of-plane forces, such as the apico-basal cable in apoptotic cell [@Monier:2015, @Gracia:2019] or lateral tension [@Sherrard:2010, @Sui:2018]. Modeling these processes help us understand how tissue acquire their shape, in complement of the experimental systems, and beyond their limitations. Several vertex models have been developed in the past few years to describe the physics of epithelia (for a review, see [@Alt:2017]), and common features can be identified. Several kinds of models have already been published. The apical vertex model has been used several times to study topology changes during morphogenetic movement in _Drosophila, Hydra and Xenopus_([@Staple:2010], [@Farhadifar:2007], [@Aegerter:2012]). Associated with protein dynamics, it has been used to study the effect of protein position on tissue organisation in zebrafish retina ([@Salbreux:2012]). 3D vertex model have been used to study epithelium deformation due to normal development or to cancer development ([@Okuda:2015], [@Eritano:2020]). Most of the time, models are developed for a specific biological question and are difficult to adapt to an other system, for severals reasons. However, there is some exception like Chaste [@Cooper:2020], which propose an open source C++ library to model cell populations or how specific events arise at the system level. With the `tyssue` library, we propose models which are adaptable and scalable with the fied research and the biological question. Topology and mechanics are implement independantly to improve the versatility of models.
 
 The `tyssue` library defines epitheliums as meshes. A vertex model defines a tissue as an assembly of vertices and edges, which can form polygonal face (in 2D) or polyhedron (in 3D). For now, we assume that cell junction are straight lines. In `tyssue`, each edge is split, so that every face is limited by oriented "half-edges" (see figure 1 A), in a structure identical to the [Linear Cell Complex](https://doc.cgal.org/latest/Linear_cell_complex/index.html) in the CGAL library. The `tyssue` library  allows to produce different kinds of tissue, from 2D to 3D tissue (see figure 1 B). The library implements concepts and mechanisms common to all vertex models, for both topological and mechanical aspects.