This is the README file for the Particle-based model associated with the paper:

Denizot, A., Arizono, M., Nägerl, V., Soula, H., Berry, H. (2019). Simulation of calcium signaling in fine astrocytic processes: effect of spatial properties on spontaneous activity. 

This model is implemented in C language and requires make build automation tool.
This model corresponds to the Particle-based model presented in Fig2, 3, 4 and 5 of the paper (see also Material & Methods section for more information on the different models developed).


HOW TO RUN THE CODE 
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List of all files that are necessary to run the code:

cell.c & cell.h: initializes cell and then describes all reactions that can happen per time step.

cl1000.map: example of receptor map, in which the 1000 IP3R are uniformly distributed within simulation space.

clist.c & clist.h: functions to deal with calcium and ip3 lists.

d4s_spont.c: main file, that sets parameter values, initial conditions and runs the simulation for a given number of time steps. Data is printed at each time step as follows:  time, nb of free Ca, nb of IP3, nb of open IP3R. Data is printed at every dt (time step).
To run the simulation you have to provide 5 arguments: map of IP3R (ie the coordinated of the 1000 IP3R molecules, one molecule per line), Dca, Dip3, gamma, seed value

Makefile

param.h: list of parameters in the model

part.c & part.h: defines how a particle (Ca or IP3) is defined in the model + related functions

receptor.c & receptor.h: defines how a receptor is defined in the model + related functions

utils.c & utils.h: useful functions for pseudo-random number generation. 


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First, you need to build. Command:  
make
Then, you can run a simulation. Example command:
./d4s_spont.out cl1000.map 0.1 10.0 100 1 > partic_based.1000.1   



Contact:
audrey.denizot@inria.fr