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Table 5 Common visualization tool overview

From: In silico approach in reveal traditional medicine plants pharmacological material basis

Tools Websites Features References
CADLIVE http://www.cadlive.jp CADLIVE (Computer-Aided Design of LIVing systEms) is a comprehensive computational tool for constructing large-scale biological network maps, analyzing the topological features of them, and simulating their dynamics [89]
Cytoscape http://www.cytoscape.org Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data [90]
Graphviz http://www.graphviz.org Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains [91]
Pajek http://www.mrvar.fdv.unilj.si/pajek Pajek is a program package for analysis and visualization of large networks (networks containing up to one billion of vertices, there is no limit-except the memory size-on the number of lines). It has been available for 20 years [92]
VANTED http://www.vanted.ipkgatersleben.de VANTED is a tool for the visualization and analysis of networks with related experimental data. Data from large-scale biochemical experiments is uploaded into the software via a Microsoft Excel-based form. Then it can be mapped on a network that is either drawn with the tool itself, downloaded from the KEGG Pathway database, or imported using standard network exchange formats. Transcript, enzyme, and metabolite data can be presented in the context of their underlying networks [93]
VisANT http://www.visant.bu.edu/ VisANT is an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package [94]
YANAsquare http://www.yana.bioapps.biozentrum.uni-wuerzburg.de YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network performance analysis (calculation of flux modes as well as target and robustness tests) [95]