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File Types and Usage

Files used by NeuronetExperimenter fall into two categories: those that are needed before building the simulator, and those used when running the simulator. Consult the conventions for how to read these files.

Building the Simulator

    ODEN files (*.oden) - describe the mathematical equations and parameters that define the behavior of each neuron type  

    connection_type_files - this specifies how neurons you create are allowed to communicate with one another

Running the Simulator

    Network file (*.net) - describes how the neurons within a network are connected and each neuron's specific parameter values.

    Experiment file (*.exp)describes what actions should occur over a range of time. This can be used by the simulator                                                                                                          to change parameter values or connectivity of the network during a run of the simulator

    Setup file (*.setup) - describes which experiments to run, and how many times, and how they should be run
                                                                 (e.g., time step, simulation duration)

    Adjacency/latency matrix files - detail the connectivity you want to exist between neurons

    Variable network files - allows for testing large numbers of networks with otherwise identical parameters with relative ease

    Input_files - variables whose value you wish to be retrieved from a file during a simulation   

File Types and Usage Conventions

Throughout this manual we will use this set of conventions:

1. { } indicates that what is in the text is not literal; that is, you have to put whatever the text inside the {} means

2. A * will indicate any number of whatever text or item immediately preceeds it

3. x | y indicates that x or y can be here (not both though)

4. [x | y] z indicates that z always follows x and y, which can be present here
5. < > indicates that whatever is in brackets is strictly optional
6. Comments are allowed anywhere in any files.  They can be indicated by #,//, or the C-style of /* */
7. A name with a
-statement  after it means that the what goes there is a statement, the definitions of which will be supplied after name-statement:
8. Anything in italics without a -statement after it is a comment to the reader
9. Text in
Courier font explicitly indicates text you will write literally into the files.

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