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
Required: ODEN files (*.oden) - describe the mathematical equations and parameters that define the behavior of each neuron type Optional: connection_type_files - this specifies how neurons you create are allowed to communicate with one another Running the Simulator
Required: 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)Optional: 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.