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. Available nmrML compliant tools are here listed as follows: (Tool Category, Tool name, Key Functions, URL, Developer)
Format Converters
nmrML converter (Java)
Converts vendor to nmrML format:
Development code on git at:
https://github.com/nmrML/nmrML/tree/master/tools/Parser_and_Converters/Java
Table with Vendor format parameter to nmrML element mappings:
https://docs.google.com/spreadsheets/d/1ZnPmqYZBuI8755UNePRBwVJnLGIQB7D-bO7voA65noU/edit#gid=0
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:
Leibniz Institute of Plant Biochemistry (IPB), Germany
Based on the OpenMS/TOPP code
Spectrum Viewers
JSpectraViewer (JSV)
Interactive NMR Spectral Viewer used in tools such as Bayesil and nmrML-Assign:
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:
The Metabolomics Innovation Center (TMIC), Canada
nmrML-Assign
nmrML conversion, annotation and peak assignment to compounds for reference spectra:
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:
University of Calgary (U of C), Canada
rNMR
Region-of-interest based NMR spectra quantification:
University of Calgary (U of C), Canada
MetaboLab
High-throughput pre-processing for Matlab driven NMR statistics:
University of Birmingham (UBir), United Kingdom
Statistics Tools
MetaboAnalyst
Statistical post-processing:
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
PhenoMeNal Containers
App library for PhenoMeNal Galaxy Workflow integration:
