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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
JournalBioinformatics
Volume30
Issue23
Pages3440-2
Date Published2014 Dec 01
ISSN1367-4811
KeywordsDocumentation, Nanoparticles, Neoplasms, Reproducibility of Results, Research Design, Software
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.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=25150250
DOI10.1093/bioinformatics/btu554
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/25150250?dopt=Abstract

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