ProteoLens: A Database-Driven Visual Data Mining Tool for Network Biology

Abstract

Systems biology studies require researchers to understand how myriads of biomolecular entities orchestrate with one another in concert to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decades to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. In this chapter, ProteoLens, a powerful visual analytic software tool for creating, annotating, and exploring multi-scale biological networks is introduced. ProteoLens is a stand-alone software tool written in Java programming language. The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced in relational database management to perform large-scale integrated network visual explorations. It presents biological network in multiple different types of layout such as organic and hierarchical methods. And the users can use queries to specify and store “associations” between nodes as “interaction” or as nodes’ annotation/edges’ annotations. Then associations can be used to visually annotate large displayed biological networks using node/edge shape, size, weight, color, and text. In the below, we describe design ideas, whole architecture, and the major operations of this software and show some case studies to demonstrate how it is used to solve multi-scale biological network questions in details.