NESim Help

Neural Engineering Simulator (NESim) Help
The Simulator The first window you see on startup is the simulator window. This window controls the overall behavior of the simulation once the neural populations have been generated, and the system has been defined. File Menu Open Settings...: This reads in a previously saved file that defines all parameters in the simulation. Save Settings...: This constructs a .mat file that can be opened later which saves all of the parameters currently set in the simulation. Save Settings and Results...: This constructs a .mat file that can be loaded later that saves all of the parameters currently set in the simulation as well as the current output plots.   File Information File Name: This is the name of the file that stores the data necessary for the simulator to run. This file and filename are generated based on what has been defined in the editor. If you newly define or change a .txt file in the editor, you must press the Setup Sim button to generate the .mat file. Load: Pushing this button loads the named .mat file that has been generated by the NESim compiler. (The compiler runs when you press the Setup Sim button). Simulation Parameters Length of Run: This is the length of time (in seconds) that the system will be simulated for once the 'run simulation' button is pressed. Time Step: This is the time step used for running the simulation. If this time step is too large, and spiking neurons are being used, an error might be generated (and displayed in the Matlab main window). Like most numerical simulations, there are no straightforward rules for picking the best time step. Noise Level: This is the variance of the noise introduced into the simulation at run time. Generally, this should match the noise used to generate the neural ensembles, but this does not need to be the case. Random Seed: If this is set to -1, then a random run will occur (i.e., random noise). For a given positive value, the random seed in Matlab's random number generator is set to the value. This allows for the exact replication of simulations which have noise. Simulation Method Ensemble: This is the name of the ensemble for which the simulation method is defined. This information is loaded from the .mat file. Simulation Method: This determines to what degree of neural plausibility a given simulation is run. 'No Neuron Encoding' results in quick run times, but does not represent the vectors in a neural population. This is useful for first tests of a simulation but not for detailed modeling. 'Activities' means that rate neurons are used in the simulation. This is more neurally plausible that 'No Neuron Encoding', but is more computationally demanding. 'Spikes' uses the defined spiking neuron model, is the most neurally plausible and the most computationally demanding. All Activities/Spikes: Pressing the appropriate radio button changes all ensembles to spikes or activities. No radio button indicator means there is a mix of simulation methods. External Inputs Pressing this button opens the signal generator. Connection Parameters Connection: This is the name of the connection for which the subsequent parameters are defined. This information is loaded from the .mat file. Synaptic Time Constant: This is the time constant (in seconds) for all synapses bewteen the sending and receiving populations. In future releases, there will be more flexibility in defining this variable (i.e. different time constants for each neuron connection). Filter Order: This is the 'n' in the equation that defines the (normalized) postsynaptic current generated by the arrival of an action potential. A larger number results in a smoother postsynaptic current. The equation is: . Plots Select Plots: This button opens the plot selector. Close Plots: This button closes all open plots (no matter which program opened them). Execution Setup Sim: This runs the NESim compiler on the .txt file named at the top of the window. If the text file changes, you need to click Setup Sim before the new definition will be effective. Run Direct: This button runs the simulation with no neurons (i.e., using the vectors and synaptic time constants only). This is equivalent to setting all of the simulation methods to 'No Neuron Encoding'. This is quick and useful for preliminary testing of the simulation. Run: This button runs the simulation defined by the parameters in this window. The results are plotted according to the contents of the 'Data Plots' tab.