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/ | ||