Examples
Here are some quick tutorials on how to do specific things in
Simbrain. The basics of building a network and other
simple examples are covered in the quick-start.
Plot the activation of a node over time with a time-series plot.
Create a neural network and a time series plot. You will now creating a coupling
from a node in the neural network to a time series in the
plot. The easiest way to do this is as follows. Right
click on the node whose activation you want to plot, and in the context
menu go to Send coupling to > TimeSeriesPlot1 > Series0.
(TimeSeriesPlot1 is the name of the time series plot. If you have
multiple plots open it might be a different name. Series0 is a
particular time series in the plot.) By repeating this for
different nodes you can plot the activation of multiple neurons at
once. If you want to add more time series beyond the default 5, click "add" in the time series component.
Now run your simulation and you should see a plot of the changing activation of the neuron. For some purposes it helps to turn "auto range" off in the time series preferences, and manually set upper and lower bounds.
Plot the activation of a set of nodes using a project plot and the coupling manager
(There are other ways to do this, some of them simpler in some cases, but this technique also shows you how to use the coupling manager). This assumes a network component is open in the desktop.
1) Open a projection plot. To
do this either press on the plot button in the
desktop toolbar, which opens up a drop down menu with different plot
components, or use the menu Insert > New Plot >...
Then select projection plot. The will add a projection plot to
your desktop with a default name like "Projection 1".
2) Open the coupling manager using the Couplings > Open Coupling Manager button.
3) On the left panel of the coupling manager, use the top drop down box
(which allows you to select components) to select the network whose
activity you want to plot.
4) On right panel of the coupling manager, select the plot component you added to the desktop in step 1, e.g. "Projection 1".
5) In the left panel, highlight rows corresponding the neurons whose
activity you are
interested in plotting (do this by clicking on rows while holding the
shift key down). Neurons are labelled by ids. To
find the neurons' ids in the network window you can hover over them and
look at the tooltip.
6) In the right panel of the coupling manager, highlight all the
"dimension" attributes either using the mouse or by pressing command-a
while that panel is in focus.
7) Click "add couplings" at the bottom of the coupling manager window.
Now when you run the workspace each new network state should produce a point in the projection plot.
Note that if you plot more than 25 neurons you will have to add more
dimensions to the projection plot using the add dimension button in the
projection plot, or the menu Edit > Set dimensions... If you use less than 25 neurons you don't have to reset the projection plot but you can if you'd like.
Train a 2-layer network on a pattern association task
For now see the preliminary trainer docs.