Next: The drug editor Up: XNBC8 User Manual V8.21 Previous: The simple network editor

The full featured network editor

The name of the full featured network editor is network_editor.

XNBC has a simple network builder, the simple network Link Editor provides the basic features to create the files needed by the simulation:

Nucleus creation
Generic intra- and inter-clusters links creation
Neuron to neuron connecting ability

The simple network editor provides only connection in excite, inhibit or randomized mode and does not take the cluster repartition into account.

The need of the spatial functionality for the network builder made the simple network editor unable to do spatial organisation of the network. Nuclei and clusters are not spearated: the cluster is only a group of neurons of the same kind (same neuron file). This is often enough, this why the simple network editor is still distributed within XNBC.

New concepts bring by the full featured network editor

The new concepts came out with the need of a 3D network representation. The cluster concept met here its limits:it is only a cast of neuron , which no real spatial meaning.

Inspired from the brain geometry, comes now the nucleus concept. A nucleus has a spatial meaning: it is made of neurons that can be from several different clusters, and that are placed together in a same area. So, the new network builder include several editors , that work a different levels :

The Network Editor, the main editor, where you can find nucleus, neurons and connections between them.
The nucleus editor, which works at the nucleus level.
Other editors , like neuron or generic link editor, and so on.

User interface of the full featured Network Editor.

According to the nucleus concept and the spatial 3D representation, the user interface is made of several windows as follows:

The main window called the Network Editor including the network 3D view area and all its relative functions (Fig. 6.1)

Figure: The full featured network editor working space
$\begin{figure}\centerline{\psfig{file=net_ed_vue.ps,width=10cm}} \end{figure}$
The nucleus editor window called Nucleus Editor including the nucleus 3D view area and all its relative functions (Fig. 6.2)

Figure: The full featured network editor nucleus editor
$\begin{figure}\centerline{\psfig{file=net_ed_partial.ps,width=15cm}} \end{figure}$
The nucleus parameters dialog box called Nucleus Parameters providing a dialog that can modify nucleus parameters (Fig. 6.3)

Figure: The full featured network editor Nucleus Parameters dialog box
$\begin{figure}\centerline{\psfig{file=net_ed_generic.ps,width=8cm}} \end{figure}$
The nucleus composition dialog box called Nucleus Composition providing a dialog for adding clusters to a nucleus in generic editing mode
The neuron parameters dialog box called Neuron Editor providing a dialog box for modifying the neuron parameters
The simple neuron to neuron link editor dialog box called Single Link Editor that fixes the single neuron to neuron link values such as the axon length for instance
The adjusting connectivity curve editor called Connectivity Curve providing in case of partial generic connection a way to weight the connection repartition according to the nucleus anatomy (Fig. 6.4).

Figure: The full featured network editor connection curve editor
$\begin{figure}\centerline{\psfig{file=net_ed_courbe.ps,width=15cm}} \end{figure}$
The generic link and connection matrix editor window called Connection Matrix Editor including the 2D matrix view of one particular generic link (Fig. 6.5)

Figure: The full featured network editor Connection Matrix editor
$\begin{figure}\centerline{\psfig{file=net_ed_mat.ps,width=15cm}} \end{figure}$

**Figure:** **The full featured network editor working space**
$\begin{figure}\centerline{\psfig{file=net_ed_vue.ps,width=10cm}} \end{figure}$

**Figure:** **The full featured network editor nucleus editor**
$\begin{figure}\centerline{\psfig{file=net_ed_partial.ps,width=15cm}} \end{figure}$

**Figure:** **The full featured network editor Nucleus Parameters dialog box**
$\begin{figure}\centerline{\psfig{file=net_ed_generic.ps,width=8cm}} \end{figure}$

**Figure:** **The full featured network editor connection curve editor**
$\begin{figure}\centerline{\psfig{file=net_ed_courbe.ps,width=15cm}} \end{figure}$

**Figure:** **The full featured network editor Connection Matrix editor**
$\begin{figure}\centerline{\psfig{file=net_ed_mat.ps,width=15cm}} \end{figure}$

The 3D views are in fact 3 2D views figuring a 3D Horsley Clarke coordinates system. A popup menu allows the user to switch between the different L-H, L-AP and AP-H views (the Horsley Clarke coordinates system is inspired from the brain geometry: L for lateral, H for height and AP for antero-posterior, the origin being in the middle of the axe joining the two ears).The L-H view is called the Front View, the L-AP the Horizontal View and the AP-H is called the Sagittal View. In addition to that, there are two other functionnalities implemented: the ability of redefining the origin in the work area (note that all distance are expressed in millimeters) and also making zooms in or zooms out in each view. The Look and Feel of the full featured Network Editor follows the concepts of the Motif Style Guide, giving in that the warranty that the user can not loose the control of his work as he already worked with other Motif designed applications. The object orientation is also respected: the user selects the neuron or whatever he wants to select before to invoke any actions on the selected item.

The Help on line is implemented at all the levels of the tool certifying that the user always know which action to invoke or the steps to follow before invoking actions. A Help on context is also implemented, providing a dynamic help library to allow new topics to be included, such as neuron types documentation or specific biological topics.

PostScript representation of networks are possible through the File Menu/Print (Fig. 6.6).

**Figure:** **A PostScript hard copy of a network**
$\begin{figure}\centerline{\psfig{file=hybride_net.ps,width=10cm}} \end{figure}$

Links between neurons and between nuclei

Links (axons) can be established either on a global basis, or individually.

On the network window, links are indicated by a colored line (red: excitatory, blue: inhibitory and green: random -a mix of both excitatory and inhibitory connections). The color of the nucleus indicates the type of ontra nucleus connection. A single neuron with a color indicates a recurrent connection of the color type.

On the nucleus window, each individual interneuron links are indicated with the same color code. The color intensity indicates the relative weight (between max and min weight in the nucleus).

Each neuron can be moved to be positioned at the right anatomical position (in the 3D space).

Network concept

A network is made of one or several nuclei and one or several isolated neurons.

A nucleus is made of several neurons. These neurons can pertain to different clusters.

A neuron is a neural entity that has a particular physical type, and has a specified location.

It is of course a real concept. The neurons are the basis of the neural activities.

Four different models are implemented:

the Conductance Based Model of neuron (CBM), a Hodgkin-Huxley like model with 14 different transmembranar currents
the Phenomenologic Model of neuron (PUM), a phenomenologic model with adaptation and post spike membrane shunt.
the Leaky Integrator Model of neuron (LIM), classical.
the Burster Unit Model of neuron (BUM), a phenomenologic model of conditional burster with adaptation and post spike membrane shunt.
the Virtual (not simulated by the simulator) model stored in a file and coming from either a live experiment or a previous simulation. This model allows to made hybrid networks made of simulated neurons receiving inputs from neurons experimentally recorded.

Nucleus concept

The nucleus is a new abstract concept introduced with XNBC V8.0.

It is a convenience object to design a group of neurons ( belonging to clusters) that have the same location area, specified by a center and a radius arround this center. This concept introduces the spatial influence in the networks interactions and allows to take into account

the anatomic location of neurons (the Horsley Clarke coordinates can be used)
the connection according to the inter neuron distance
the connection pattern
the dissociation of anatomical location and unit characteristics
the neuromodulator or drug concentration according to the production or injection locus (in a future version of XNBC)

Files

Input: *.lnk, .net_customrc

Output: *.len, *.wgt, *.clu, *.anat, *.lnk, *.ps, .net_customrc

Known problems

There is no known problems, but this tool is probably the most complex, and can appear as little bit complicated to use.

Next: The drug editor Up: XNBC8 User Manual V8.21 Previous: The simple network editor

Jean-Francois Vibert
1998-08-26