patternMorph

This repository is meant for code used to model a range of patterning and morphogenetic phenomena in biology.

To run this code you need to download and install deal.ii from the website: www.dealii.org. Then clone this repo, and add a CMakeLists.txt in your local patternMorph/ folder. You can simply copy CMakeLists.txt from any of the deal.ii example folders. For instance, if you copied CMakeLists.txt from the example1 folder, modify the following line in CMakeLists.txt:

SET(TARGET “example1”) --> SET(TARGET “diffusionAndMechanics10”)

Then run the following commands:

cmake CMakeLists.txt

make

Please consider citing the following paper. This code was used to run all the numerical examples in the paper, and is being refactored constantly. So, check back in a few weeks and it’s usability will be progressively improved.

@article{Garikipati2016,

title = {Perspectives on the mathematics of biological patterning and morphogenesis},

author = {Garikipati, K.},

journal = {Journal of the Mechanics and Physics of Solids},

volume = {99},

pages = {192-210},

doi = {10.1016/j.jmps.2016.11.013},

archivePrefix = “arXiv”,

eprint = {1610.02584},

primaryClass = “q-bio”,

Year = {2017}
}