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

Bioinformatics
Authors
Keywords
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.

Year of Publication
2014
Journal
Bioinformatics
Volume
30
Issue
23
Pages
3440-2
Date Published
2014 Dec 01
ISSN
1367-4811
URL
DOI
10.1093/bioinformatics/btu554
PubMed ID
25150250
PubMed Central ID
PMC4296150
Links
Grant list
R01 GM089652 / GM / NIGMS NIH HHS / United States