Metabolomics Visualization

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More than one level of visualization can be recognized:

  • raw data
  • intermediate data (to check pre-processing results)
  • preprocessed data
  • modelling results
  • pathways
  • networks (i.e., biological relationships beyond metabolic pathways)

Data Types

Data types that need to be visualized include:

  • 1D spectra: NMR, MS, chromatograms
  • 2D spectra: hyphenated spectra of various kinds, 2D NMR?
  • 3D chemical structures
  • 2D diagrams for chemical structures
  • Spectral trees: multiple 1D spectra with a hierarchical grouping
  • Metabolic Pathways

Libraries versus Standalone Tools

It is important to realize that visualization tools need to be integrated into the support platform. This poses the following requirements on possible tools suggested below:

  • uses open standard file formats
  • must integrate with workflow platforms and/or web interfaces
  • license must allow integration

Integration is typically easier when the software is available as library, instead of a standalone application.

Open Source tools

Pathway/Network visualization

Possible tools that could be integrated are described here.

  • pathvisio, an open source biological model construction tool built by the Maastricht University bioinformatics dept.
  • cytoscape, the well-known network building tool.
  • osprey Network vizualisation software.
  • ARM computer tracing of atomic positions in metabolism]
  • MSFACTs alignment of GC/MS and LC/MS data and visualisation.
  • MetaboClique Network visualisation by grouping cliques.
  • Biocyc, Metacyc, Pathway Tools Software. BioCyc and Metacyc contain collections of Pathway/Genome DBs that provide electronic reference sources on the pathways and genomes of different organisms. Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology:
   * Development of organism-specific databases (also called model-organism databases) that integrate many bioinformatics datatypes, from genomes to pathways.
   * Scientific Visualization, web publishing, and dissemination of those organism-specific databases, including:
         o Automatic display of metabolic pathways and full metabolic networks
         o A genome browser
         o Display of operons, regulons, and full transcriptional regulatory networks 
   * Visual analysis of omics datasets, such as painting omics data onto diagrams of the full metabolic network, full regulatory network, and full genome
   * Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, and prediction of operons, that can be used for genome analysis
   * Comparative analyses of organism-specific databases
   * Analysis of biological networks:
         o Interactively tracing metabolites through the metabolic network
         o Finding dead-end metabolites in metabolic networks
         o Identifying choke points (potential drug targets) in metabolic networks 

see Pathway Tools Information Site for the Perl/Java/Lisp APIs

Applets / Web integration

Commercial/Proprietary tools

Possible tools that could be integrated are described here.

  • Metacore from genego is until now the best visualisation and bioinformatics tool for creating annotated biological networks. It is used by several consortia and hosted at a TNO server for web-access. NMC can obtain a floating licence.

Open source applications