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

Khan, Imtiaz, Fraser, Adam, Bray, Mark-Anthony, Smith, Paul J., White, Nick S., Carpenter, Anne E. and Errington, Rachel 2014. ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinformatics 30 (23) , pp. 3440-3442. 10.1093/bioinformatics/btu554

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Abstract

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 http://protocolnavigator.org/index.html under the GPL v2 license.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Neuroscience and Mental Health Research Institute (NMHRI)
Subjects: R Medicine > R Medicine (General)
Publisher: Oxford University Press
ISSN: 1367-4803
Date of Acceptance: 11 August 2014
Last Modified: 31 Jul 2020 02:04
URI: http://orca.cf.ac.uk/id/eprint/79041

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