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# CellGPU
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CellGPU implements GPU-accelerated algorithms to simulate off-lattice models of cells. Its current
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two main feature sets focus on a Voronoi-decomposition-based model of two-dimensional monolayers
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and on a two-dimensional dynamical version of the vertex model. CellGPU grew out of DMS'
"DelGPU" and "VoroGuppy" projects, and the current class structure still bears some traces of that
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(please see the contributing page of the documentation, which is maintained at
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https://dmsussman.gitlab.io/cellGPUdocumentation
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for information on upcoming code refactoring and new planned features). The paper describing this
code in more detail can currently be found on the arXiv (https://arxiv.org/abs/1702.02939), or in print (
http://www.sciencedirect.com/science/article/pii/S0010465517301832)
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Information on installing the project and contributing to it is contained in the relevant
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markdown files in the base directory and in the doc/markdown directory. Documentation of the
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code is maintained via Doxygen, which can be viewed at the gitlab.io pagea linked to above, or by compiling
the doxygen documentation in the "/doc" directory
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A very rough outline of some of the main classes and the basic operating flow of the primary branches
of the code can be found [here](@ref basicinfo); this page is a good place to start before diving into
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the code (Please note that if you are reading this on the Gitlab main page the links will not work...
visit the main documentation page at https://dmsussman.gitlab.io/cellGPUdocumentation or compile
Doxygen documentation locally).
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By default cellGPU includes a few different classes, mostly using the netCDF format, for saving simulation
data. For convenience, a few Mathematica scripts demonstrating how to load these files and turn them
into simple visualizations are included in the visualizationTools directory -- these should be readily
portable to matlab, python, etc.

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## Project information
Here are some convenient links to a variety of general information about the cellGPU project; all
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of the below can also be accessed from the @ref projectInfo tab (links work on the gitlab.io
documenation website)
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[Basic class overview](@ref basicinfo)
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[Installation guide](@ref install)
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[Sample code snippets](@ref code)
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[Contributing to cellGPU](@ref contrib)
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[Citations](@ref cite)
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[Open-source information](@ref license)
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[cellGPU version information](@ref changelog)
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[Contributors](@ref contributorList)