title: Extracting patterns of database and software usage from the bioinformatics literature.
abstract: BACKGROUND
  As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools.
  
  
  RESULTS
  We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice.
  
  
  METHODS
  The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/.
authors.affiliation: School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK.
authors.forename: Geraint
authors.initials: G
authors.lastname: Duck
authors.affiliation: School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK.
authors.forename: Goran
authors.initials: G
authors.lastname: Nenadic
authors.affiliation: School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK.
authors.forename: Andy
authors.initials: A
authors.lastname: Brass
authors.affiliation: School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK.
authors.forename: David L
authors.initials: DL
authors.lastname: Robertson
authors.affiliation: School of Computer Science, Manchester Institute of Biotechnology and Computational and Evolutionary Biology, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Stevens
mesh_terms: D019295:Computational Biology; D057225:Data Mining; D016208:Databases, Factual / Q000706:statistics & numerical data*; D010506:Periodicals as Topic; D010802:Phylogeny; D012984:Software