1. Visualization of Organism-Scale Metabolic Networks

  2. Please take the BioCyc online survey

1. Visualization of Organism-Scale Metabolic Networks

One of the most popular parts of Pathway Tools is the Cellular Overview tool for visualizing organism-scale metabolic networks. This recent publication from SRI's Bioinformatics Research Group surveys the development of this tool as it has matured along multiple dimensions:

  • From manual layout of the diagram to automatic layout

  • From a single organism to 18,000 organsisms

  • From unicellular organisms to multi-cellular organisms, pan-genomes, and organism communities

  • From slower tiled zooming to real-time zooming

  • Evolution of the diagram to become an interpretation device for transcriptomics and metabolomics data

"Pathway Tools Visualization of Organism-Scale Metabolic Networks"
Metabolites 2021, 11, 64.

2. BioCyc Survey

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