CADLIVE Converter for constructing a biochemical network map
In systems biotechnology biochemical network maps are the essential bases for analyzing their topological features and for simulating their dynamic behaviors. Most of network data are available at public databases, relating to gene expression, protein–protein interaction, and metabolic pathways. On the other hand, since those databases use a variety of data formats, computational tools always require the conversion of such database formats into their available format. In this work, we developed a GUI-based WWW browser program, which converts different databases (KEGG, RegulonDB, DIP, etc.) into the format available to our CADLIVE system, integrates a variety of network data into a fully functional pathway map, and visualizes the integrated map. This program is named the CADLIVE Converter. We demonstrated the feasibility and availability of it by performing metabolic pathway analysis and dynamic modeling. The visualization of the network map lead to an intuitive understanding of topological architecture of complex networks.
► We develop the CADLIVE Converter as a new extension of our CADLIVE system. ► Efficient, direct connection of various databases to CADLIVE. ► Easy handling of complex, heterogeneous network data. ► High efficiency for data integration, pathway analysis and dynamic modeling. ► Fast layout and visualization of an integrated map.
Journal: Biochemical Engineering Journal - Volume 54, Issue 3, 15 May 2011, Pages 200–206