Building and Editing Networks

Network editing in Simbrain is modeled on a familiar "draw" interface which involves creating screen elements, copying, and pasting.

Creating Nodes

Creating a node: Nodes are created by pressing "P" or by pressing the new node button in the toolbar. Any new nodes will be created at the last position clicked on-screen.

Creating a line of nodes: Repeatedly pressing "P" or the new node button results in a line of nodes being created beginning at the last clicked position.

Creating specific types of neurons: By default, new nodes are Linear. The default node type cannot currently be changed, though this is planned. To create a node of a specific type, simply create a new node, right click the node, then go to "Edit 1 Selected Neuron". From there one can select any neuron type in Simbrain from a dropdown menu.

Creating many nodes: To create many nodes at once one can go to Insert > Add Neurons and instantly create an arbitrary number of neurons specified in the Add Neurons window. Upon closing windows requesting information on the type and layout of the neurons will appear. Information on laying out groups of neurons can be found on the Layouts page. Alternately, to create many nodes of a specific type one can:

Create a node, set its type (as specified above), and then copy and paste repeatedly.
  OR
Create many default nodes, select all of them with the cursor (see Selecting Nodes and Weights below), right click any of them, and change their type from: Edit N Selected Neurons, where N is the number of selected neurons.

Creating networks or groups of nodes: Subnets are created using Insert > Add Network. Subnetworks and small groups of neurons can be created, copied, and repeatedly pasted to quickly create many sets of similar elements.

Zooming and Panning

To zoom use the mouse-wheel or the pinch-to-zoom gesture on trackpads. To pan press the command or control key while left-clicking and dragging. Note that by default auto-zoom is turned on; if you plan to zoom in and pan a lot it should be turend off. To fit all objects on screen hit the "F" key to invoke the zoom to fit command.

Selecting Nodes and Weights

Neurons and weights can be selected so that operations can be performed on the selected group of items (e.g., randomizing selected items, adjusting them up or down, etc.). Selecting neurons and weights is important, because many Simbrain operations apply to selected sets of weights and/or nodes. The selection interface basically works the way most computer drawing programs work. Use the left-click button to "lasso" or "rubberband" screen items. Once some items are selected, you can hold down the shift key and single-click to fine tune your selection.

Selection mode: All selection operations must be done in selection mode, the default mode, which is entered by pressing "S" or the selection button .

Lasso: Left-click and drag the lasso around screen items you want to select. As items are selected a box appears around them.

Single click: Single left-click on nodes and weights to select individual screen items. Zooming in on items can facilitate this.

Shift key : Once some items are selected, you can hold down the shift key to add more items to your selection. Hold down Shift while lassoing to add or remove groups items; hold down Shift while single-clicking to add or remove single items.

Setting Properties

Some detailed properties are set using a dialog box. Other properties, e.g. activation values for neurons and strengths for weights, can be set using keyboard and toolbar commands.

Calling set properties dialog: Select the neurons or weights you want to change and:

1) double-click on of the selected items
2) right-click and select set properties in the popup menu
3) select network > edit > set neurons or network > edit > set weights

Setting properties of multiple objects. Select the objects you want to modify. If you select both weights and neurons, which preference dialog comes up depends on which kind of item you click on.

Set activation values: The activation value (and hence color) of neurons and the excitatory or inhibitory strength (and hence color and size) of weights can be manually adjusted. To do so, select one or more neurons and weights (both can be adjusted at the same time), and press the up and down arrow keys to increase or decrease these values. The amount increased or decreased is set by the "increment" field. Right and left arrow keys can also be used to increase or decrease these value.

Clearing and randomizing values: Note that while screen items are selected, neuron values can also be set to zero by pressing "C" on the keyboard (weight values are not then set to zero, because this is equivalent to deleting them, which can be done with the delete key). Pressing "R" will randomize all selected screen items, neurons and weights.

Moving Nodes

Simply left click and drag the selected items, as you would a window or any other screen item. Groups of items can be moved by selecting and left-click dragging them. For fine tuning, users can also use the arrow keys (with Shift held down) to "nudge" selected items.

Smart copy and paste

Selected items can be copied, cut, and paste similarly to the way they are on most contemporary GUI's. Lasso select groups of items, then fine tune your selection using SHIFT to add or remove items. Simbrain will automatically select all valid subnetworks (all nodes and all selected connections which couple selected nodes; i.e. "free-floating" connections will not be selected).

Copy, copy, and paste in one of the following ways

1) Use standard shortcuts: control-C (copy), control-X (cut), control-V (paste).
2) Use the network menu and select copy, cut, or paste.
3) Right-click on one of the selected items and select copy or cut

Smart copy/paste: Copy neurons, paste, move, and re-paste, and the new paste’s follow the rule. In this way you can quickly build big networks.