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. 2014 Nov 4;5:598. doi: 10.3389/fpls.2014.00598

Table 1.

List of software discussed in this review: Network tools for metabolic system biology analysis and related data formats.

Software name Description Supported data formats (built-in annotation data) Interface/ Language Reference/Author name URL
NETWORK AND PATHWAY ANALYSIS TOOL
igraph Library for the analysis of networks. It supports topological- and centrality analysis. (in most cases) adjacency list, edge list, GraphML R, Python, C/C++ http://igraph.org/index.html
Networkx A Python language software library for the analysis of networks. This package supports topological- and centrality analysis. (in most cases) adjacency list, edge list, GraphML, json Python http://networkx.github.io/
CentiScaPe Centralities analysis plug-in for Cytoscape. Java Scardoni et al. (2014) http://apps.cytoscape.org/apps/centiscape
CentiLib Centralities analysis plug-in for VANTED. Java Gräßler et al. (2012) http://centilib.ipk-gatersleben.de/
BiNGO Gene ontology enrichment analysis plug-in for Cytoscape. Java Maere et al. (2005) http://apps.cytoscape.org/apps/bingo
FluxMap FBA plug-in for VANTED. Java Rohn et al. (2012a) http://vanted.ipk-gatersleben.de/addons/fluxmap/
Enrichment Map A Cytoscape app/plug-in to perform and visualize pathway/gene set enrichment analysis. Java Merico et al. (2010) http://apps.cytoscape.org/apps/enrichmentmap
Network visualization
Cytoscape A widely used biological network analysis platform. This software supports many biological network data formats and its visual appearance is fully customizable. The 'NetworkAnalyzer' default plug-in computes basic properties of the whole network. A huge number of plug-ins is available from the Cytoscape App Store. In contrast to VANTED, this software does not support KGML by default. SBML, BioPAX, edge list, PSI-MI Java Smoot et al. (2011) http://www.cytoscape.org/
KEGGscape A Cytoscape plug-in for KGML import. KGML Java Nishida et al. (2014) http://apps.cytoscape.org/apps/keggscape
VANTED Along with Cytoscape, a popular network analysis software that also supports many biological network data formats. Its visual appearance is fully customizable. SBML, BioPAX, edge list, KGML, DOT Java Rohn et al. (2012b) http://VANTED.ipk-gatersleben.de/
Kappa-View A web-based correlation network viewer on metabolic pathway maps. User's own omics data (AraCyc version8) Java Sakurai et al. (2011) http://kpv.kazusa.or.jp/
MapMan The view is not a network graph, but it is useful for displaying omics data onto diagrams of metabolic pathways or other processes. User's own omics data (MapMan ontology) Java Usadel et al. (2005) http://mapman.gabipd.org/
Pathview An R/Bioconductor package for pathway-based data integration and visualization. Bioconductor compliant data R Luo and Brouwer (2013) http://www.bioconductor.org/packages/release/bioc/html/pathview.html
GeneMANIA A web-based interaction network (including physical and genetic interactions, and co-expression and prediction networks) viewer. Also accessible via a Cytoscape plug-in. Gene list Java Montojo et al. (2014) http://genemania.org/
CellDesigner A software for browsing and modifying existing SBML models. SBML Java Funahashi et al. (2008) http://www.celldesigner.org/
PathVisio Pathway drawing and analysis tool for WikiPathways (http://www.wikipathways.org). GPML Java Van Iersel et al. (2008) http://www.pathvisio.org/
Data format
KGML XML for the KEGG PATHWAY database (available without the KEGG FTP academic subscription). Commonly used to reconstruct a KEGG pathway network layout. It can be used for the visualization of pathway maps of a multitude of different organisms. Kanehisa et al. (2014) http://www.kegg.jp/kegg/xml/
BioPAX General format for pathway data. It is defined in OWL and represented in the RDF/XML format. Its main focus is data exchange and integration. Demir et al. (2010) http://www.biopax.org/
SBML Tuned and commonly used format for mathematical models of biological networks/pathways. Almost all metabolic reconstructions are written in this format. Hucka et al. (2003) http://sbml.org/
PSI-MI Suitable format for representing details about molecular-, especially protein-protein interaction data. Arabidopsis Interactome Mapping Consortium data are distributed in this format. Van Roey et al. (2013) https://code.google.com/p/psimi/