UserGuide:Neurobrowse

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Neurobrowse: An interactive graphical browser for neural networks.

Introduction:

Wormbase stores information about anatomical connections of neurons, based on the reconstruction of electron micrographs of serial sections. Neural connections form networks which can be explored using Neurobrowse. It is an adaptation of N-Browse, designed for displaying gene interaction networks.

Neurobrowse is an Java Web Start application that can be launched directly via this Neurobrowse URL. Alternatively, Neurobrowse is linked on specific Anatomy Term pages in WormBase.

Neurobrowse 20101101.jpg

Basic operations:

1. To start a query, one enters a cell name in the "New Search:" box, at the upper left corner of the NBrowse window, and click the green GO button. For example, one queries for R2AR, a neuron in the male sensory ray.

2. To reduce the complexity of the network view, one can click on the button "Spoke View Only". This reduces the visible connections to those directly involves R2AR.

3. Mousing over a specific node in the network brings up information about that node in the Info widget (lower left corner) with a URL link back to the relevant WormBase anatomy page.

4. Clicking on the Edge Table (lower left bottom) reveals all the connections in the graph. In particular, the "Cut off" column indicates the number of times a specific connection was observed. A connection may be less reliable if it has not observed for more than one time.