title: ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.
abstract: BACKGROUND
  Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments.
  
  
  METHODS
  ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license.
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Imtiaz A
authors.initials: IA
authors.lastname: Khan
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Adam
authors.initials: A
authors.lastname: Fraser
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Mark-Anthony
authors.initials: MA
authors.lastname: Bray
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Smith
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Nick S
authors.initials: NS
authors.lastname: White
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Carpenter
authors.affiliation: School of Medicine, Cardiff University, Cardiff, UK, Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA and School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.
authors.forename: Rachel J
authors.initials: RJ
authors.lastname: Errington
mesh_terms: D004282:Documentation; D053758:Nanoparticles / Q000032:analysis; D009369:Neoplasms / Q000737:chemistry; D015203:Reproducibility of Results; D012107:Research Design; D012984:Software