Software Tools for Systems Biology: Visualizing the Outcomes of N Experiments on M Entities

Chris Poultney, Dennis Shasha

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Systems biology deals with genes, proteins, ions and other molecular entities. It involves the integrated analysis of these molecular entities from many experiments conducted under different conditions. This common feature - many treatment conditions and thousands or more entities - poses a challenge to finding the answers to natural questions such as: Which subsets of conditions yield similar outcomes? Which entities respond similarly in many conditions? and Which functional groupings of entities are most affected by which conditions? In this chapter, we describe a visualization tool to help answer these questions, complementary informatic tools to support alternate visualizations, and explore the lessons learned in constructing that tool both fromthe software designer's and biologist's perspective.

Original languageEnglish (US)
Title of host publicationPlant Systems Biology
PublisherBlackwell Publishing Ltd
Pages167-195
Number of pages29
Volume35
ISBN (Electronic)9781444312249
ISBN (Print)9781405162838
DOIs
StatePublished - Aug 18 2009

Keywords

  • Experiments
  • Genome
  • Interface
  • Systems biology
  • Visualization

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

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  • Cite this

    Poultney, C., & Shasha, D. (2009). Software Tools for Systems Biology: Visualizing the Outcomes of N Experiments on M Entities. In Plant Systems Biology (Vol. 35, pp. 167-195). Blackwell Publishing Ltd. https://doi.org/10.1002/9781444312249.ch5