NESim Help

Neural Engineering Simulator (NESim) Help
About the Neural Engineering Simulator (NESim) The NESim environment is for constructing large-scale simulations of neurobiological systems. It is based on the framework and methodology described in detail in Eliasmith and Anderson (2003) Neural Engineering: Computation, Representation and Dynamics in Neurobiological Systems (MIT Press; see here for more information). This code was developed from that used to construct the examples provided in this book. However, it is not quite as general as the approach described there. NESim includes two main parts: a GUI and a main engine written in Matlab. This documentation describes the use of the GUI, although the source for both the GUI and the engine are included in the download (for some more advanced applications, it may be useful to use and/or modify the engine code directly). Main Features Enables rapid construction and testing of large-scale models Includes multiple (easily extensible) single neuron models Supports high-dimensional vector encoding in neural populations Supports linear and nonlinear functional transformations (upto 5th order) Includes built-in signal generator for comprehensive testing with various inputs User definable input signals in .mat (Matlab) format (useful for simulations using previously collected data). Plots currents, soma voltages, activities, spike rasters, population-level representations and 'ideal' solution as desired. System Requirements Matlab 6 or later (untested in earlier versions). Installing and Running NESim 1. To install NESim, download the package from here, and unzip the contents into any folder on your system (the Matlab 'work' folder is appropriate). This will create the NESim directory and its subfolders. 2. Setting the Matlab Paths The Matlab path must include all of the files used by NESim. To make sure this is the case, execute the commands: addpath '<full path of install directory>/subs' addpath '<full path of install directory>/NeuronData' Then goto File->Set Path... and click the 'save' button so it isn't necessary to repeat these steps every time Matlab is restarted. 3. Starting NESim Simply type 'NESim' at the Matlab command prompt. Note that it is often easier to first proceed to the directory where your simulations reside before starting the program. For the examples, this is the 'Simulations' directory. When searching for files, NESim first looks for the simulation data in the current directory (e.g. Simulations), once that is found it looks for the neuron data in the current directory (e.g. Simulations). If no neuron data is found in the current directory, it then searches the path for a 'NeuronData' directory and uses the files there. This means there are two standard ways to use NESim: 1. Have all files for a given simulation (i.e. simulation definition, and neuron data) in one directory and work in that directory. 2. Have simulation definitions in one directory (the directory you must be in to run the simulation), and the neuron data in another directory (i.e. the NeuronData directory on the path). This makes it easy to reuse neuron data across various simulations.