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V.1 Tutorial 1: definition of an abstract network

Figure 1 showed an almost empty model, and it fills more than an A4 page ! Therefore the scripting of full models can become a very long and boring task. This is why the GuiKit has been developed. It allows the quick definition of NeuroML files. The GuiKit allows mapping an interface on a user defined object. Run NMLPlay as explained in section II.B of this user guide. The following window will appear (Figure 5).

Figure 5: The main window of NMLPlay.

This window will be referred as the networks panel. In this first tutorial, a simple abstract network will be created. ?Abstract? means that it can not be input in the simulator. A few default objects are part of this model. The grid with a brown texture will be called the network design panel. The sub-panel called the display options panel allows to disable the display of the grid/texture. There is the menu panel on the right of the network design panel. The green rectangle in the top of the menu panel allows the creation of neural populations (the type of neurons needs then to be specified). The blue rectangle allows the definition of probes. "HodgkinHuxleyNeuron" is an item which allows the creation of neurons whose spiking activity corresponds with the Hodgkin-Huxley model. Just below is an item which allows nesting a copy of network0 in another network. Below is an item called ImplementationNeuron. This item allows creating a population of Integrative neurons. There are two arrows below, a blue one which allows the creation of inter-neurons connections and a yellow arrow which allows the creation of connections between neurons and probes.

If the mouse pointer is moved over the menu panel, the item under the pointer turns red. That means that it can be selected. Please move the pointer over the population node NewPop. Left-click on it and release the left button. Move the mouse pointer to the grid panel and left-click on it. When the left button is released, a new population is added on the grid panel. If you click on it with the wheel of your mouse (or central button), you can drag the population node on the grid. The new population is called NewPop0. Please add another population node to the grid in the same way. It will be called NewPop1. Now a new projection (a set of inter neurons connections) can be added by left-clicking on the projection link Projection (blue arrow), releasing the left button, moving the mouse pointer to the grid panel, and left-clicking again. When the left button is released, a new projection link is added on the grid panel. The added projection link is called Projection0. There are three green spots on Projection0. These green spots are also called control points. They determine the shape of the arrows. This shape can be changed. Move the mouse pointer to one of these control points. Click on it with the central button of the mouse (or the wheel) and drag it over the editing panel. If the selected spot is the middle control point, the entire arrow moves. If it is one of the two ends of the arrow, Projection0  is reshaped.

A projection is supposed to connect two population nodes, one being the source and the other one the target. To select the target of Projection0, move the control point on the arrow end of Projection0 to NewPop1 as learned previously. Once NewPop1 is hit, it should turn white. You can then release the central button. The target of Projection0 is now NewPop1. Select the control point at the other end of Projection0. Move it to Population0, which turns white when it is hit. Release the central button. The source has been selected. Now if you select the central spot on the arrow and move it around, only this spot should be moving and the 2 others are stuck to the population nodes. If the population nodes are moved, the corresponding control points on Projection0 will follow their population nodes. The window should look like Figure 6.

Figure 6: A simple abstract network.

When a network includes hundreds of populations, some basic functionalities, such as zooming or navigating through the grid will be very useful. To zoom in, left-click on an empty part of the grid. To zoom out, right-click on an empty part of the grid. To navigate through the grid, right-click on an empty point of the grid, hold the button pressed and drag around your mouse pointer, the grid will follow the move. A population node or a projection link can be removed by clicking on "Remove" on the editing window which appear after double-clicking on an item. Adding elements increments the index the newly created component. Therefore, it is possible that you have different element indices from the ones provided in the following tutorials.

You have built your first network. You can now quit by clicking the red button with a cross on the upper right corner of the current and main windows.