The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads to a change of state in the cell. Pathways come in different flavors, depending on their functions in the cell – the three main types are metabolic pathways, gene regulatory pathways, and signaling pathways. These biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization.
Following are the comprehensive list of visualization tools for biological pathways:
BiNA
Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures
BioTapestry
Interactive tool for building, visualizing and sharing gene regulatory network models over the web
Caleydo
Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets
CellDesigner
A modeling tool for biochemical networks
Edinburgh Pathway Editor
Edit and draw pathway diagrams
http://epe.sourceforge.net/SourceForge/EPE.html
GenMAPP
Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes
Ingenuity IPA
Data integration platform and manually annotated pathways
http://tinyurl.com/IngenuityPath
JDesigner
Graphical modeling environment for biochemical reaction networks
http://jdesigner.sourceforge.net/Site/JDesigner.html
KaPPA View
Plant pathways
KEGG Atlas
Interactive Kyoto Encyclopedia of Genes and Genomes pathways
Omix
Visualizing multi-omics data in metabolic networks
https://www.omix-visualization.com
PathVisio
Biological pathway analysis software that allows drawing, editing and analysis of biological pathways
VitaPad
Application to visualize biological pathways and map experimental data to them
Web tools for pathways
ArrayXPath
Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG
http://tinyurl.com/ArrayXPath/
GEPAT
Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts
iPath
Web-based tool for the visualization, analysis and customization of pathway maps
Kegg-Based Viewer
KEGG-based pathway visualization tool for complex high-throughput data
http://www.g-language.org/data/marray/
MapMan
User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes
http://mapman.gabipd.org/web/guest/mapman
MetPA
Analysis and visualization of metabolomic data within the biological context of metabolic pathways
Omics Viewer
Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)
Pathway Explorer
Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them
http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml
Pathway projector
Zoomable pathway browser using KEGG atlas and Google Maps API
http://www.g-language.org/PathwayProjector/
PATIKA
Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework
http://www.cs.bilkent.edu.tr/~patikaweb/
Reactome SkyPainter
Visualization of over-represented pathways and reactions from gene lists
http://www.reactome.org/skypainter-2
WikiPathways
Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community
