This code is associated with the paper from James et al., "Modelling the emergence of whisker barrels". eLife, 2020. http://doi.org/10.7554/eLife.55588

BarrelEmerge

This is a simulation of the growth of axons which demonstrates how the whisker barrel field pattern can selforganize in the presence of only two orthogonal molecular guidance cues. It is the code behind the following paper:

James, Krubitzer & Wilson. 2020. Modelling the emergence of whisker barrels. eLife. DOI: https://doi.org/10.7554/eLife.55588

The emergence of whisker barrels is demonstated in a modified Karbowski-Ermentrout-like axon branching population model.

For instructions on reproducing the results of the paper, see the README.md file in the scripts subdirectory.

Before you do that, you'll need to build this simulation code, which is compiled against our library of research software, morphologica. So, first, obtain and build morphologica (it has its own README.md with instructions). morphologica can be obtained here on github:

https://github.com/ABRG-Models/morphologica/tree/papers/BarrelEmerge_eLife

(Note that I've linked to you a particular branch of morphologica, in case any future changes there break the compilation of this version of BarrelEmerge).

Once you've compiled and installed morphologica, you can compile BarrelEmerge:

cd BarrelEmerge
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

Note: You'll ideally have an OpenMP-capable compiler. You'll probably need libomp as well, because even though my code doesn't use the runtime part of OpenMP, Armadillo does so if OpenMP is present. You get OpenMP/libomp for free with gcc on a modern Linux computer; on a Mac, you will have to install libomp from source (follow instructions at https://openmp.llvm.org/ finishing up with a final make install).

Now you can read how to reproduce the experiments. To reproduce all of the results, see ./scripts/README.md. To graph the resulting data, see ./analysis/README.md.

To reproduce, and simultaneously view, the main result, as presented in Fig. 1C, you can run one simulation:

./build/sim/james_comp2 ./configs/rat/41N2M_thalguide_Fig1.json

Note: The simulation is computationally demanding. It takes about 11 minutes to run the 50000 steps of Fig. 1C simulation on a 6-core gaming laptop (with an 8th gen Intel Core i9 processor and with the code compiled with OpenMP to use all the cores). An older, 6th gen Core i5 laptop (2 cores) needed 23 minutes for the same simulation.

If you have any trouble, please post an issue on github at https://github.com/ABRG-Models/BarrelEmerge/issues and I will do my best to help.

Seb James, September 2020.