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BMC Bioinformatics. 2015 Jun 20;16:197. doi: 10.1186/s12859-015-0637-6.

RDML-Ninja and RDMLdb for standardized exchange of qPCR data.

Author information

1
Department of Anatomy, Embryology & Physiology, Academic Medical Center, Amsterdam, 1100AZ, Netherlands. j.m.ruijter@amc.uva.nl.
2
Center for Medical Genetics, Ghent University, Gent, B-9000, Belgium. steve.lefever@UGent.be.
3
Bioinformatics Institute Ghent, Ghent University, Ghent, B-9000, Belgium. steve.lefever@UGent.be.
4
Center for Medical Genetics, Ghent University, Gent, B-9000, Belgium. jasper.anckaert@UGent.be.
5
Bioinformatics Institute Ghent, Ghent University, Ghent, B-9000, Belgium. jasper.anckaert@UGent.be.
6
Biogazelle, Zwijnaarde, 9052, Belgium. Jan.Hellemans@Biogazelle.com.
7
Physiology, Center of Life and Food Sciences, Technical University of Munich, Freising Weihenstephan, Munich, 85354, Germany. michael.pfaffl@wzw.tum.de.
8
Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, 69117, Germany. benes@embl.de.
9
Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford, CM1 1SQ, UK. stephen.bustin@anglia.ac.uk.
10
Center for Medical Genetics, Ghent University, Gent, B-9000, Belgium. Joke.Vandesompele@UGent.be.
11
Bioinformatics Institute Ghent, Ghent University, Ghent, B-9000, Belgium. Joke.Vandesompele@UGent.be.
12
Biogazelle, Zwijnaarde, 9052, Belgium. Joke.Vandesompele@UGent.be.
13
Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, 69117, Germany. andreas@untergasser.de.
14
Center of Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 282, Heidelberg, 69120, Germany. andreas@untergasser.de.

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.

PMID:
26087842
PMCID:
PMC4474546
DOI:
10.1186/s12859-015-0637-6
[Indexed for MEDLINE]
Free PMC Article

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