title: Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.
abstract: BACKGROUND
  Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported.
  
  
  RESULTS
  We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users.
  
  
  BACKGROUND
  http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive), ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download).
  
  
  CONCLUSIONS
  From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools.
authors.affiliation: Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia. a.garcia@imb.uq.edu.au
authors.forename: Alexander
authors.initials: A
authors.lastname: Garcia Castro
authors.forename: Samuel
authors.initials: S
authors.lastname: Thoraval
authors.forename: Leyla J
authors.initials: LJ
authors.lastname: Garcia
authors.forename: Mark A
authors.initials: MA
authors.lastname: Ragan
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D003195:Computer Communication Networks; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D030541:Databases, Genetic; D016247:Information Storage and Retrieval; D015233:Models, Statistical; D008962:Models, Theoretical; D009323:Natural Language Processing; D009862:Online Systems; D011381:Programming Languages; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D012985:Software Design; D013997:Time Factors; D014584:User-Computer Interface