[1] Brocke, E., Bhalla, U. S., Djurfeldt, M., Hellgren Kotaleski, J., & Hanke, M. (2016). Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations. Frontiers in Computational Neuroscience, 10, 97. http://doi.org/10.3389/fncom.2016.00097 [2]
################################################################################ Hierarchy of folders ################################################################################ . ├── createfigures : contains scripts for reading and plotting the results. See plotme.m scripts in the data folder. │ ├── createfigure.m │ └── read_multirate_datapoints.m ├── data : contains *.mat object data files to generate figures in [1,2]. Each subfolder contains plotme.m script to generate the figure. │ ├── multirate : multirate datafiles [2] │ │ ├── Figure1 │ │ ├── Figure2 │ │ └── Figure3 │ └── refsol : contains *.mat data files with the reference solution │ ├── ode15s_v2 │ └── ode15s_v3 ├── model_v2 : electrical-chemical model with the fast communication signal, calcium is solved on the biochemical side │ ├── common │ ├── hh : electrical multicompartmental model with HH currents │ ├── kkit : biochemical MAPK model │ ├── modelconst.mat │ ├── save_consts.m │ ├── sim_combine2j2.m : can be used to obtains the solution with ode15s │ └── yTypicalSolution.txt ├── model_v3 : electrical-chemical model with the slow communication signal, calcium is solved on the electrical side. │ ├── common │ ├── hh : electrical multicompartmental model with HH currents │ ├── kkit : biochemical MAPK model │ ├── modelconst.mat │ ├── save_consts.m │ ├── sim_combine2j2.m : can be used to obtain the solution with ode15s │ └── yTypicalSolution.txt ├── README.md └── solvers : contains implementation of the adaptive and fixed stepsize solvers ├── methods : numerical integration methods ├── sim_combine2j2.m : implements MAIN function of the coupled integration
################################################################################ To run ################################################################################
sim_combine2j2.m has to be called to start the simulation. Parameters of interest can be assigned inside sim_combine2j2.m:
- MODEL : name of the model to simulate. Default: MODEL='model_v3'.
- iterMethod : can be one of {'Jac','GSCELLFirst','GSERKFirst','GSSlowFirst','GSFastFirst'}. Default: iterMethod = 'GSSlowFirst'.
- multirate : <true, false>. Default: multirate = true.
- slv_param : tolerance value (or the number of steps for a fixed step size controller). Default: slv_param = 1e-5.
- T_SIM : simulation time. Default: T_SIM = 2 [s].
- solvErkNM, solvCellNM : reference to the numerical method. Default: solvErkNM = solvCellNM = @BDF2_DEF.
- odeslv : reference to the solver. Default: odeslv = @adaptive_solver.