Construction and Visualization of Dynamic Biological Networks: Benchmarking the Neo4J Graph Database

Abstract

Genome analysis is a major precondition for future advances in the life sciences. The complex organization of genome data and the interactions between genomic components can often be modeled and visualized in graph structures. In this paper we propose the integration of several data sets into a graph database. We study the aptness of the database system in terms of analysis and visualization of a genome regulatory network (GRN) by running a benchmark on it. Major advantages of using a database system are the modifiability of the data set, the immediate visualization of query results as well as built-in indexing and caching features.