Data integration is a central activity in systems biology. The integration of genomic, transcript, protein, metabolite, flux, and computational data yields unprecedented information about the system level functioning of organisms. Often, data integration is done purely computationally, leaving the user with little insight besides statistical information. In this article, we present a visualization tool for the metabolic network of Synechocystis PCC6803, an important model cyanobacterium for sustainable biofuel production. We illustrate how this metabolic map can be used to integrate experimental and computational data for Synechocystis systems biology and metabolic engineering studies. Additionally, we discuss how this map, and the software infrastructure that we supply with it, can be used in the development of other organism-specific metabolic network visualizations. Besides a Python console package VoNDA (http://vonda.sf.net), we provide a working demonstration of the interactive metabolic map and the associated Synechocystis genome-scale stoichiometric model, as well as various ready-to-visualize microarray data sets, at http://f-a-m-e.org/synechocystis/.
Additional Metadata
Keywords Visualization, Synechocystis, FBA, Metabolic Modeling
THEME Life Sciences (theme 5), Energy (theme 4)
Publisher American Society of Plant Biologists
Journal Plant Physiology
Citation
Maarleveld, T.R, Boele, J, Bruggeman, F.J, & Teusink, B. (2014). A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803. Plant Physiology, 164, 1–11.