1. Introduction

BiologicalNetworks has been designed to model whole cell biochemical pathways and gene regulatory networks. BiologicalNetworks uses a specialized graph visualization engine to represent biological pathways, gene regulation networks and protein-protein interaction maps for intuitive exploration and prediction. The software can handle a variety of tasks, including graphic drawing and layout optimization, data filtering and pathway expansion, and classification and prioritization of proteins. BiologicalNetworks uses a proprietary file format (BNX or BiologicalNetworks model XML format) that stores information pertaining to the model and the corresponding simulation environment in BiologicalNetworks. BiologicalNetworks supports import and export of models from the System Biology Mark-up Language (SBML), SIF and GML file formats. The following is a summary of the functionality of BiologicalNetworks: Distribution BiologicalNetworks is a freely distributed Java-based web application. BiologicalNetworks network annotation is stored in an XML-based file. Users can run and obtain the software in three ways: 1. Run the online BiologicalNetworks Applet Save the XML files in secure online workspace, share with other users. 2. Run the full BiologicalNetworks Java Web-Start Application. Includes ability to save and read XML files on local machine, read netwo