ChiBE: Interactive visualization and manipulation of BioPAX pathway models

Ozgun Babur, Ugur Dogrusoz, Emek Demir, Chris Sander

Research output: Contribution to journalComment/debate

29 Scopus citations

Abstract

Summary: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large pathway datasets requires software that can combine data mapping, querying and visualization as well as providing access to diverse data resources on the Internet. ChiBE is an open source software application that features userfriendly multi-view display, navigation and manipulation of pathway models in BioPAX format. Pathway views are rendered in a featurerich format, and may be laid out and edited with state-of-the-art visualization methods, including compound or nested structures for visualizing cellular compartments and molecular complexes. Users can easily query and visualize pathways through an integrated Pathway Commons query tool and analyze molecular profiles in pathway context. Availability: http://www.bilkent.edu.tr/%7Ebcbi/chibe.html. Contact: ugur@cs.bilkent.edu.tr Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)429-431
Number of pages3
JournalBioinformatics
Volume26
Issue number3
DOIs
StatePublished - Dec 9 2009

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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