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. 2015 Jun 20;16(1):197.
doi: 10.1186/s12859-015-0637-6.

RDML-Ninja and RDMLdb for Standardized Exchange of qPCR Data

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Free PMC article

RDML-Ninja and RDMLdb for Standardized Exchange of qPCR Data

Jan M Ruijter et al. BMC Bioinformatics. .
Free PMC article

Abstract

Background: The universal qPCR data exchange file format RDML is today well accepted by the scientific community, part of the MIQE guidelines and implemented in many qPCR instruments. With the increased use of RDML new challenges emerge. The flexibility of the RDML format resulted in some implementations that did not meet the expectations of the consortium in the level of support or the use of elements.

Results: In the current RDML version 1.2 the description of the elements was sharpened. The open source editor RDML-Ninja was released (http://sourceforge.net/projects/qpcr-ninja/). RDML-Ninja allows to visualize, edit and validate RDML files and thus clarifies the use of RDML elements. Furthermore RDML-Ninja serves as reference implementation for RDML and enables migration between RDML versions independent of the instrument software. The database RDMLdb will serve as an online repository for RDML files and facilitate the exchange of RDML data (http://www.rdmldb.org). Authors can upload their RDML files and reference them in publications by the unique identifier provided by RDMLdb. The MIQE guidelines propose a rich set of information required to document each qPCR run. RDML provides the vehicle to store and maintain this information and current development aims at further integration of MIQE requirements into the RDML format.

Conclusions: The editor RDML-Ninja and the database RDMLdb enable scientists to evaluate and exchange qPCR data in the instrument-independent RDML format. We are confident that this infrastructure will build the foundation for standardized qPCR data exchange among scientists, research groups, and during publication.

Figures

Fig. 1
Fig. 1
Open source editor RDML-Ninja. a Target information is displayed after selection of an ID in the left section. b The annotation and results of a single plate are visualized in an interactive table view. c Amplification results and melt point measurements can be plotted in a graph and exported in SVG format. A high resolution image is available as supplemental data
Fig. 2
Fig. 2
Search interface of RDMLdb. RDML files are found in the database based on query key elements

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References

    1. Lefever S, Hellemans J, Pattyn F, Przybylski DR, Taylor C, Geurts R, Untergasser A, Vandesompele J. RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Res. 2009;37:2065–2069. doi: 10.1093/nar/gkp056. - DOI - PMC - PubMed
    1. Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ and Moorman AF. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009; A37:e45. doi: 10.1093/nar/gkp045 - PMC - PubMed
    1. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007;8:R19. doi: 10.1186/gb-2007-8-2-r19. - DOI - PMC - PubMed
    1. Rödiger S, Burdukiewicz M, Blagodatskikh KA, Schierack P. R as an Environment for the Reproducible Analysis of DNA Amplification Experiments. The R Journal. 2015;7:1–24.
    1. Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A. A survey of tools for the analysis of quantitative PCR (qPCR) data. Biomolecular Detection and Quantification. 2014;1:23–33. doi: 10.1016/j.bdq.2014.08.002. - DOI - PMC - PubMed

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