title: Methodology for constructing problem definitions in bioinformatics.
abstract: BACKGROUND
  A recurrent criticism is that certain bioinformatics tools do not account for crucial biology and therefore fail answering the targeted biological question. We posit that the single most important reason for such shortcomings is an inaccurate formulation of the computational problem.
  
  
  RESULTS
  Our paper describes how to define a bioinformatics problem so that it captures both the underlying biology and the computational constraints for a particular problem. The proposed model delineates comprehensively the biological problem and conducts an item-by-item bioinformatics transformation resulting in a germane computational problem. This methodology not only facilitates interdisciplinary information flow but also accommodates emerging knowledge and technologies.
authors.affiliation: Département de Biochimie, Université de Montréal, Robert Cedergren Center for Bioinformatics and Genomics, Montréal, Québec H3T 1J4, Canada. amy.hauth@umontreal.ca
authors.forename: Amy M
authors.initials: AM
authors.lastname: Hauth
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger