Tools supporting nmrML

The nmrML development team has also fostered and coordinated the creation of nmrML aware webservices and tools covering a large fraction of a typical NMR data acquisition and processing workflow, i.e. to generate, convert, process, validate and publish nmrML files. Additionally, we have worked closely with open source and commercial tool developers to encourage nmrML format adoption. A summary table of available nmrML compatible tools is available below.

Tool Category

Tool name

Key Functions

URL

Developer

Format Converters

nmrML converter (Java)

Converts vendor to nmrML format

https://github.com/nmrML/nmrML/tree/master/tools/Parser_and_Converters/Java

Institut National de la Recherche Agronomique (INRA), France

nmrML converter (Python)

Converts vendor to nmrML format

https://github.com/nmrML/nmrML/tree/master/tools/Parser_and_Converters/python/pynmrml

The Metabolomics Innovation Center (TMIC), Canada

nmrML to ISA converter

Generate pre-populated ISA files from nmrML files

https://github.com/ISA-tools/nmrml2isa

Ecole Normale Supérieure de Cachan (ENS Cachan), France

Parsers

Matlab parser

Matlab functions parsing and decoding nmrML files, and also writing Maltab data into nmrML format.

https://github.com/nmrML/nmrML/tree/master/tools/Parser_and_Converters/Matlab

Imperial College London (ICL), United Kingdom

nmRIO

R package for parsing and decoding nmrML files

https://github.com/nmrML/nmrML/tree/master/tools/Parser_and_Converters/R/nmRIO

Leibniz Institute of Plant Biochemistry (IPB), Germany

Data Validators

nmrML semantic validator

XML Schema compliance and rule-based validation of CV usage

http://nmrml.org/validator/

Leibniz Institute of Plant Biochemistry (IPB), Germany

Spectrum Viewers

JSpectraViewer (JSV)

Interactive NMR Spectral Viewer used in tools such as Bayesil and nmrML-Assign

http://nmrml.bayesil.ca

The Metabolomics Innovation Center (TMIC), Canada

NMR Processing, Identification & Quantification tools

NMRProcFlow

An interactive 1D NMR spectra processing tool dedicated to metabolomics

http://nmrprocflow.org/b_introduction

Institut National de la Recherche Agronomique (INRA), France

Bayesil

Automated compound identification, quantification and annotation

http://bayesil.ca, http://tmic.bayesil.ca

The Metabolomics Innovation Center (TMIC), Canada

nmrML-Assign

nmrML conversion, annotation and peak assignment to compounds for reference spectra

http://nmrml.bayesil.ca

The Metabolomics Innovation Center (TMIC), Canada

Batman

Bayesian deconvolution and automated quantification of metabolites

http://batman.r-forge.r-project.org

Imperial College London (ICL), United Kingdom

Metaboquant

Peak-integration-based spectrum quantification and outlier detection

http://www.uni-regensburg.de/medicine/statistical-bioinformatics/software/software-from-gronwald-group/metaboquant/index.html

University of Calgary (U of C), Canada

rNMR

Region-of-interest based NMR spectra quantification

http://rnmr.nmrfam.wisc.edu

University of Calgary (U of C), Canada

MetaboLab

High-throughput pre-processing for Matlab driven NMR statistics

http://metabolab.uk

University of Birmingham (UBir), United Kingdom

Statistics Tools

MetaboAnalyst

Statistical post-processing

http://www.metaboanalyst.ca

The Metabolomics Innovation Center (TMIC), Canada

Workflow Tools

SOMA:tameNMR

NMR data processing and analysis via Galaxy Workflows

https://github.com/pgb-liv/tameNMR

University of Liverpool (UoL), United Kingdom