Synapses
Synapses, also known as weights, are represented in Simbrain by a colored semicircle. The size of the semicircle is proportional to how far the synaptic strength is between 0 and its upper or lower bound. The exact strength can be determined by lingering over a synapse or double clicking on it. The color of a synapse represents whether the strength is: greater than 0, red; less than 0, blue; or equal to 0, white. The last case represents, as it were, the absence of a weight. These conventions can be adjusted in the preference dialog.
Setting Synapse Properties
To set a single synapse, double click or right click on it and select set properties. Since synapses are relatively small, you can either zoom in or lasso the synapse of interest.
To set multiple synapses, select more than one synapse, and either double click on one of the synapses you have selected, or select set properties from the popup or network menu. A dialogue box pertaining to multiple synapses will appear. If the selected neurons are of different synapse types, only the common properties appear. Consistent properties are shown as normal, while inconsistent properties have "..." in the text box. Any changes, including changes to the fields where parameters have been marked as inconsistent, are applied to all of the selected neurons.
Common Synapse Properties
These are properties common to all synapses, regardless of type. All of them have some reflection in the GUI interface, but some of them only matter to the GUI interface (e.g. increment). For some synapses, upper bound and lower bound does not have a significant role other than to limit how larget the graphical representation of the synapse can be.
Strength: The strength is how "strong" this synapse is. This is represented by the size of the weight. Once a synapse has been selected, strength can be incremented by the up and down arrows or can be randomized.
Increment: The increment field sets the amount that a synapse is incremented when it is manually adjusted. For example, if increment is set to .1, then each time the up arrow is pressed the synapse will increase its strength by .1.
Upper Bound : This field plays different roles depending on the type of the synapse, but in general it determines the maximum strength of a weight. It also determines the range of colors which a neuron can take on. This, along with the lower bound field, determines the bounds of randomization.
Lower Bound : This field, like the upper bound, plays different roles depending on the type of the synapse, but in general it determines the minimum strength of a weight. It also determines the range of colors which a neuron can take on. This, along with the upper bound, determines the bounds of randomization.
Delay: A positive integer that delays how many iterations, or time-steps, must occur before the pre-synaptic signal, or the activation of the pre-synaptic neuron, is delivered.