title: Pathway collages: personalized multi-pathway diagrams.
abstract: BACKGROUND
  Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions?
  
  
  RESULTS
  We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts. The user specifies a set of pathways of interest for the collage from a Pathway/Genome Database. Layouts for the individual pathways are generated by the Pathway Tools software, and are sent to a Javascript Pathway Collage application implemented using Cytoscape.js. That application allows the user to re-position pathways; define connections between pathways; change visual style parameters; and paint metabolomics, gene expression, and reaction flux data onto the collage to obtain a desired multi-pathway diagram. We demonstrate the use of pathway collages in two application areas: a metabolomics study of pathogen drug response, and an Escherichia coli metabolic model.
  
  
  CONCLUSIONS
  Pathway collages enable facile construction of personalized multi-pathway diagrams.
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.affiliation: John Innes Centre, Department of Metabolic Biology, and the Institute of Food Research, Food & Health Programme, Norwich Research Park, Norfolk, NR4 7UH, UK.|Current address: Biosciences Division, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA.
authors.forename: Paul E
authors.initials: PE
authors.lastname: O'Maille
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Weaver
authors.affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, 94025, USA. pkarp@ai.sri.com.
authors.forename: Peter D
authors.identifier: http://orcid.org/0000-0002-5876-6418
authors.initials: PD
authors.lastname: Karp
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D055432:Metabolomics / Q000379:methods*; D008954:Models, Biological; D012984:Software
chemical_list: D000900:Anti-Bacterial Agents
keywords: Metabolic pathways; Pathway diagram; Visualization