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Bioinformatics DOI:10.1093/bioinformatics/btu554

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

Publication TypeJournal Article
Year of Publication2014
AuthorsKhan, IA, Fraser, A, Bray, M-A, Smith, PJ, White, NS, Carpenter, AE, Errington, RJ
Date Published2014 Dec 01
KeywordsDocumentation, Nanoparticles, Neoplasms, Reproducibility of Results, Research Design, Software

MOTIVATION: 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.

AVAILABILITY AND IMPLEMENTATION: 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 under the GPL v2 license.


Alternate JournalBioinformatics
PubMed ID25150250
PubMed Central IDPMC4296150
Grant ListR01 GM089652 / GM / NIGMS NIH HHS / United States