Synapses work a little differently for the realistic neural module than they do for other modules.
In the other plug-ins when you draw a link between two nodes you select the type of synapse and it
is drawn between the two nodes and you can modify the properties of that synapse. Changing one of the
properties like the weight only effects that single synapse. The realistic neural module is different in
that it uses the concept of a synaptic type. You can think of these as a kind of template for a synapse.
You define the synaptic type and set its properties and then when you add a new synapse between two nodes
you select which of the types to use. So you might have 20 synapses that all use the same type definition.
If you go back and make a change to the definition then it effects all of the synapses that are
associated with that synaptic type. This makes it easier for you to keep track of the different synapses you
are using in your simulation, and allows you to make global changes to all of those synapses by simply altering
one paramter in the type definition. You can create as many types as you need.
When you draw a link between any two realistic neurons the dialog in figure 1 is shown. This dialog is
used to add, remove, and manage your synaptic types. There are three different synaptic models to choose from:
electrical, spiking chemical, and non-spiking chemical. If one of the existing types meets your needs then
select it and hit Ok, or double click it. A new synapse will appear and be selected with the properties shown like those in figure 2.
These are the properties for a spiking chemical synapse type. Notice that the properties like "Decay Rate" and "Equilibrum Potential"
do not show up in the property grid of figure 2. Instead what you get is a "Synaptic Type" property that says "Hyperpolarizing IPSP".
This tells you that this synapses uses the hyperpolarizing IPSP type as its template. Its properties are determined by that template.
If you click on this property element you can re-open the synaptic type editor dialog shown in figure 2. Once in this dialog you
can switch the synaptic type for this synapse by selecting a new type definition.
If none of the currently defined types meet your needs you can add new ones. To do this open the synaptic type editor dialog and
right click on one of the three model nodes in the tree view. These are "electrical synapses", "Spiking Chemical Synapses", and "Non-Spiking Chemical Synapses".
This will display a pop-up menu. Select the "New Synapse" item. This will add a new synapse under this model with default parameters named "New Synapse Type".
You can change the name of the new synapse by using the name property in the property grid to the right. Now you simply need to go through and configure
the properties for your new synapse. When you have things the way you want them then make sure it is selected and hit the ok button to set this as the synaptic type
for the currently selected synapse.
Alternatively, there may be an existing synapse type that is close to what you want. In this case it would be easier to clone this type and
make the few changes you need rather than configuring a blank type from scratch. To do this right click on the type that you want to clone to
display a pop-up menu. Select the "Clone Synapse Type" item. A new clone of this synaptic type is created with the name "New Synapse Type".
It has all the same parameters as the original except for its name. Now you just have to make your changes.
You can modify any of the existing synaptic types at any time. Simply open the synaptic type editor dialog and make your changes to its properties. However,
please keep in mind that you are altering every synapse that is based on this type. If you do not want to make this large scale of a change then you
may need to consider cloning the synaptic type and making your changes to it instead. This way you can split this synapse into different subgroups.
You can delete a synaptic type by right clicking on it do display the pop-up menu and selecting "Delete Synapse Type".
This will display the dialog shown in figure 3. If you are deleting a synaptic type then you must re-associate any synapses
that are currently linked to that type with a different type to prevent errors in your network. This dialog box allows you
to do this. You can use the drop-down box on the right to select the synaptic type that you want to replace this type with.
It will only allow you to replace a type with one of the same model. In other words, you can only replace a spiking chemical
synpase with another spiking chemical synapse. If you hit OK then AnimatLab will go through all of the diagrams for this organism
and replace the synaptic type for any synapses that use the type you are deleting. It will then remove that type from the
Spiking chemical synapses have two properties that can be configured on an individual basis. These are the "Conduction Delay" and
the "Synaptic Strength". These properties appear in the grid for each individual synapse instead of appearing only in the properties for the synaptic
type. See figure 2. The reason for this is that these values can be different for every single synapses. If you were required to create a new type
for every instance where the strength changes you would quickly have large numbers of types and this would actually make keeping track of
which synapse is which much more difficult than it would be if we were not using the type concept at all. Therefore, these properties can
be set on an individual basis. So you can have two synapses that use the same type, but have different strengths or delays. Spiking chemical
synapses are the only models where this feature is used.
This project was supported by: