Affiliations: Institute for Mathematics and Computing Science,
University of Groningen, Netherlands | Department of Molecular Genetics, University of
Groningen, Netherlands
Abstract: Among the various research areas that comprise bioinformatics,
systems biology is gaining increasing attention. An important goal of systems
biology is the unraveling of dynamic interactions between components of living
cells (e.g., proteins, genes). These interactions exist among others on
genomic, transcriptomic, proteomic and metabolomic levels. The levels
themselves are heavily interconnected, resulting in complex networks of
different interacting biological entities. Currently, various bioinformatics
tools exist which are able to perform a particular analysis on a particular
type of network. Unfortunately, each tool has its own disadvantages hampering
it to be used consistently for different types of networks or analytical
methods. This paper describes the conceptual development of an open source
extensible software framework that supports visualization and exploration of
highly complex genomic networks, like metabolic or gene regulatory networks.
The focus is on the conceptual foundations, starting from requirements, a
description of the state of the art of network visualization systems, and an
analysis of their shortcomings. We describe the implementation of some initial
modules of the framework and apply them to a biological test case in bacterial
regulation, which shows the relevance and feasibility of the proposed
approach.
Keywords: Gene regulatory networks, prokaryotes, visualization framework, information exploration
