TissueNets Program

BioNet program is mainly used for creating and displaying Biological Networks. In general, the following steps are used for constructing a biological network:

1- Create Nodes of the network 2- Create Links based on k-nearest neighbor algorithm (with exact solution) 3- Combine Nodes and Links and create a network in XGMML form

Once a network is created, BioNet will help you to display it. After the network is displayed, the user can zoom and rotate the network to get a better view.

BioNet defines two types of networks. The first one is just a standard network consists of nodes and links (edges) defined in a network definition file. The second type of networks is minimum-spanning trees that are generated from network definition files. BioNet gives you options to make proper selections. If the user wants to display a standard network, he/she can also display pyramidal regions by entering a cutoff point. When this option is selected, the average edge lengths that are used in pyramidal region computation will be produced in the file called “pyramidal.txt” which is fixed for now.