Some basic commands one is likely to use in the Simbrain setting are as follows:
Compare projections.
Comparing how a pattern of dots (a history of states that have occurred in the relevant network subspace) looks under different projections by using the projection drop-down menu. When selecting "Sammon" be sure to press the play button to iterate the Sammon algorithm.
Save data.
Using the File menu, save the high-dimensional data. It will automatically be saved in the simulations/gauge directory. This is useful if you spend a long time acquiring some neural network data and want to save it for a demonstration or for analysis later.
Turning each gauge on and off.
The on / off button on each gauge controls whether that gauge is accepting data or not. Note that as the network is run it will still cause the current state to show up as a red dot, even if it is turned off to new data.
Setting tolerance for new datapoints.
New points are only added to a gauge if they are considered to truly be new. This is determined by testing whether they are within a specified distance of any old points. If thy are, they are not added. This distance can be set in the preferences menu under "new point resolution."