BioNetLink - an architecture for working with network data

J Integr Bioinform. 2014 Jun 30;11(2):241. doi: 10.2390/biecoll-jib-2014-241.


The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

MeSH terms

  • Algorithms
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Computer Graphics
  • Computer Simulation
  • Gene Regulatory Networks*
  • Protein Interaction Mapping / methods
  • Protein Interaction Maps*
  • Reproducibility of Results
  • Software*
  • Systems Biology / methods*
  • Transcription, Genetic
  • Transcriptome