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RetinoTectal

A model of the self-organization of the retino-tectal projection

This model uses morphologica for visualization, which is cloned as a submodule.

To build, first install morphologica dependences, as described in morphologica's README.install.linux.md or README.install.mac.md, then follow this recipe:

# If you didn't already, then clone RetinoTectal, with the --recurse-submodules switch:
git clone --recurse-submodules https://github.com/sebjameswml/RetinoTectal.git

# If you ALREADY did a git clone *without* --recurse-submodules, then don't panic! just do:
# cd RetinoTectal
# git submodule init
# git submodule update

# Now build the software:
cd RetinoTectal
mkdir build
pushd build
cmake ..
make -j4 # or however many cores you have
# (no need to install, you'll run the simulations in place)
popd

There are actually two simulation codes in this repository. The original work was a reaction-diffusion style model found in sim/rd. The final model was an agent-based model in sim/agent/. The agent-based model was the one used as the basis for the paper.

To run the simulations described in the paper, you can run:

./scripts/paper_figures.sh