OTNET: a MATLAB tool for simulating the Oxytocin Network model

NOTE: The correct functioning of the present software under MATLAB versions earlier than 6.5 is not guaranteed, and may depend on the availability of adequate built-in functions.

 

 1) Download and unzip otnet.zip.

 

 2) Launch MATLAB, change Current Directory to the unzipped folder, then type 'start' in the prompt. This will initialize the MATLAB compiler, create all the necessary MEX files, and finally produce the following interface,

2) Click on 'Load parameters' to load a parameters file; an example can be found inside the ‘results_base’ folder. Once loaded, the values of the model parameters shown on the screen can be modified by editing the correspondent fields. The number of bundles is set on the basis of the mean number of dendrites per bundle, assuming a uniform distribution, and cannot be edited directly.

For a full list of the model’s parameters and of their values, click here.

 

3) Click on ‘Run’ to launch the simulation. All the values of the parameters which exceed the prescribed bounds will be highlighted.

 

4) As soon as the simulation is started, two figures of the type described below will appear on the screen illustrating the network topology.

The first figure (above) shows which bundles are occupied by the dendrites of each cell. The mean, minimum and maximum number of dendrites

per bundle (dpb) found in the network are also indicated.

The second figure (above) is a colour plot of the adjacency (connection) matrix for the network, with elements defined as

 

where n is the number of cells, nb is the number of bundles, and the matrices Ckij are defined in [1]. The elements of the connection matrix assume values 0, 1, or 2, depending on how many bundles are shared by the cell pair (i,j).

 

5) After a simulation has completed, a new Figure will illustrate the mean firing rate (in 1-s bins) recorded in one representative cell for each bundle (up to a maximum of 5 bundles are displayed).

 

6) At the end of each simulation, all the results are temporarily stored in the folder ‘results_temp’ where they can be accessed for visualization using VIEWDATA.

 

Buttons

 

·         VIEWDATA: starts an interface for the visualization of spike data. More details here.

 

·         Save results: stores simulation results and parameters. Pressing this button will create a new folder containing: 1) a MAT file including a cell array with the interspike intervals for each cell and a structure containing information about the network’s topology; 2) a text file with all the parameter values: 3) a copy of the source code: 4) a copy of the auxiliary data file. The names of these files are set automatically and represent the date/time of the simulation.

 

·         Export spike times: saves the spike times for all cells as a tabulated list (cells as columns).

 

·         Show OT stores: shows the temporal dynamics of the dendritic stores for a model cell (top panel) and the amount of OT released inside each bundle within 1-ms bins. These variables are recorded during a simulation every Δt milliseconds, in the interval between t1 and t2. The values of Δt, t1, and t2 can be set by editing the fields ‘Recording interval’ and ‘Recording step’ in the main simulation panel.

 

·         Show voltage traces: shows the time course of the membrane potential, v1(t), and the dynamical threshold T1(t) for cell #1.

 

·         Delete figure: deletes all figures.

 

·         Exit: closes figures and exits.

 

 

References

[1]  Enrico Rossoni, Jianfeng Feng, Brunello Tirozzi, David Brown, Gareth Leng, Françoise Moos (2006) Synchronous bursting of oxytocin neurons; emergent behaviour of a model neural network.

 

 

Last modified, 22 March 2006