Experience dependent behavior in C. elegans

Code to reproduce the simulations and figures in the following paper:

María Sol Vidal-Saez, Oscar Vilarroya, Jordi Garcia-Ojalvo, A multiscale sensorimotor model of experience-dependent behavior in a minimal organism, Biophysical Journal, Volume 123, Issue 12 (2024).

See paper for more details.

Organization

• The simulations of Figure 5, 6 and 7 of the paper are generated from figures_paper_step.ipynb.
• The simulations of Figure 9, 10 and 11 of the paper are generated from graphs_paper.ipynb.

Simulations in C++

The chemotaxis assay simulations run in C++. To run them:

1. Compile the files (with make)

mingw32-make

2. Run the executable that was generated in the previous step

./main

3. If you want to delete the .o and .exe files and re-compile, run:

mingw32-make clean

Other considerations

main.cpp

In the main.cpp file you can choose running example trajectories (#define trajectories). In this case, you will save a txt file with the column values detailed in the function PrintDetail in WormAgent.cpp for every time step of the simulation. The second option is to run several simulations (#define chem_index) and save only the last time point of the simulation to compute the chemotaxis index afterwards (with the chemotaxis_index.ipynb notebook). In this case, also a txt file is generated from the PrintDetail function.

The NaCl concentration during cultivation can be changed with the parameter "phenotype(25)" (C_breed). We explored the values C_breed=25,50,100.

WormAgent.h

You can choose between a step of NaCl (#define GRAD_STEP), or the gradient use in the paper (#define GRAD_GAUS). Beware that if you use the step concentration, you need to change the constant Preexposure to a value lower than 5000 for memory reasons.

Behavioral traces during Chemotaxis assay for different cultivation conditions

Trajectories for 10 virtual worms set in a salt gradient (#define trajectories in main.cpp and #define GRAD_GAUS in WormAgent.h) for 3 pre-assay salt cultivation.