Useful tools for data standards

 

Name of Service

Developer (COSMOS partner)

URL/ Codebase

Description

1

BATMAN

4:Imperial College London

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

BATMAN is an R package for estimating metabolite levels in Nuclear Magnetic Resonance spectral data using a specialised MCMC algorithm. It deconvolves peaks from 1-dimensional NMR spectra, automatically assigns them to specific metabolites from a target list and obtains concentration estimates. The Bayesian model incorporates information on characteristic peak patterns of metabolites and is able to account for shifts in the position of peaks commonly seen in NMR spectra of biological samples.

2

Metassimulo

4:Imperial College London

http://cisbic.bioinformatics.ic.ac.uk/metassimulo/

 

MetAssimulo is a MATLAB-based package which simulates 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties

3

MZmine_2

 

http://mzmine.sourceforge.net

 

MZmine 2 is an open-source project delivering a software for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in 2006.

4

MIDcor

7:U Barcelona

http://sourceforge.net/projects/gcmscorrection/files/?source=navbar

 

 

MIDcor (Mass Isotopomer Data corrector) is an R-based computer program designed for the extraction of “pure” 13C mass isotopomer distribution of metabolites formed from artificial 13C-enriched substrates. In addition to subtraction of natural isotope distribution from raw m/z data it examines a possible overlapping m/z peaks for several metabolites, and corrects it if such an overlapping takes place.

5

SpecView

8:MPIMP/ MPG

http://gmd.mpimp-golm.mpg.de/download/

SpecView 1.0 is an Microsoft Excel™ plugin that facilitates the presentation of deconvoluted GC-MS Spectra in Microsoft Excel. Selected MS-Spectra (format: '87:100 103:78') are normalized prior to drawing.

6

KODAMA

10:CIRMMP, Florence

http://www.kodama-project.com/tutorial.html

 

KODAMA is an innovative method to extract new knowledge from noisy and high-dimensional data, and offers a general framework for analyzing any kind of complex data in a broad range of sciences. It is particularly suited, but not limited, to cluster metabolomic data. Ref.: http://www.pnas.org/content/111/14/5117.abstract

7

mzR

11:IPB

https://github.com/sneumann/mzR/

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

8

xcms

11:IPB

https://github.com/sneumann/xcms/

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

9

CAMERA

11:IPB

https://github.com/sneumann/CAMERA/

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments

10

Rdisop

11:IPB

https://github.com/sneumann/Rdisop

Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

11

nmrML validator

11:IPB

http://nmrml.org/validator/

This service is based on the TOPP tool FileInfo. It works with nmrML using the current development versions of the schema, mapping and CV. An HTML representation of the official MSI mapping file and the CV can be found online.

12

metfRag

11:IPB

https://github.com/c-ruttkies/MetFragR

Identification of metabolites using high precision mass spectrometry. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.

13

nmRIO

11:IPB

https://github.com/sneumann/NMR-ML/tree/master/tools/Parser_and_Converters/R/nmRIO

Parser for NMR raw fid and processed data from nmrML, Bruker and Varian/Agilent

14

nmrML java converter

12:U Bordeaux

http://nmrml.org/converter/

Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors

15

Xeml interactive Designer - (Xeml-Lab)

12:U Bordeaux

https://github.com/cbib/XEML-Lab

Xeml-Lab 1.0 is a software initially developed at the Max Planck Institute in 2008-2009, in order to provide an interactive graphical interface, allowing the design of complex experiments, and the generation of machine-readable metadata files. The main goal of the XEML project was to realize a standard for the control and documentation of experimental design and growth, with a maximum of power in terms of data processing, not only to obtain reliable molecular and physiological data, but also to make plant growth metadata amenable for studies in integrative biology. To make Xeml-Lab, easily distributable on various platforms ( Windows, Mac and Linux), and to offer a wider access to this tool to the biological community, we decided to rewrite it in C++ language. The new version Called Xeml-Lab 1.0 is now available.

16

rISA

14:UOXF

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

The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported.

17

LinkedISA

14:UOXF

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

linkedISA is a package to convert ISA-TAB files into RDF data relying on different semantic frameworks (OWL ontologies). For more information, please visit the linkedISA website: http://isa-tools.github.io/linkedISA/.

18

ISATab

Viewer

14:UOXF

https://github.com/ISA-tools/ISATab-Viewer

Render from files on your web server:

Provided the files are hosted on the same server your page is running on, you can just do this to load in your ISA files. Now integrated with BMC GigaScience and allows out of box rendering of ISA-Tab formatted archives for consistent and easy content exposure of experimental metadata.

19

Biocrates

2ISA.xsl

14:UOXF

https://github.com/ISA-tools/xsl2isa

an XSL transformation allowing direct deposition from Biocrates AG software to Metabolights or publication of targeted Metabolomics data generated on the Biocrates Platform as ISA-Tab metadata.

20

nmrML python converter

external partner/ stakeholder: U Alberta

https://github.com/nmrML/nmrML/tree/master/

tools/Parser_and_Converters/python/pynmrml

pynmrML is a Python library for reading, writing and interfacing with nmrML documents. It includes nmrML bindings, nmrCV bindings, and readers and writers for several different NMR formats. It relies on the excellent NMRglue library for processing raw NMR data.