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West Coast Metabolomics Center Downloads

Wohlgemuth at server

Aggregated downloads for the overall NIH Common Fund Metabolomics Program

data and protocols available from the metabolomicsworkbench.org
all WCMC data are uploaded at that website and available from there.

 

Specific WCMC data dictionaries and standard operating protocols (SOPs)

data dictionary lipidomics

SOP biofluid extraction lipidomics  
SOP data acquisition lipidomics  
SOP data processing lipidomics

data dictionary primary metabolomics

SOP biofluid extraction primary metabolism
SOP data acquisition primary metabolites  
SOP data processing primary metabolites

data dictionary biogenic amines / specialized metabolites

SOP biofluid extraction biogenic amines / specialized metabolites
SOP biofluid data acquisition biogenic amines / specialized metabolites
SOP biofluid data processing biogenic amines / specialized metabolites

 

data dictionary bile acids  SOP bile acids
data dictionary eicosanoids   SOP eicosanoids
data dictionary steroids     SOP steroids

data dictionary flux analysis   SOP flux analysis


Pilot and Feasibility projects

call for applications

submission form template

 

Data Analysis Tools

MetaMapR

A metabolomic network analysis tool enabling the rapid construction of biochemical, structural similarity, mass spectral similarity and correlation based networks.

DeviumWeb

Multivariate data analysis and visualization tool including: statistical analysis, clustering, PCA and O-PLS.

imDEV

Multivariate data analysis and visualization add-in for MS Excel.

MetaMapp

Software tool to display biochemical and chemical relationships of metabolomic data

 

Data Processing Tools

CTS (Chemical translation service)

Software tool to convert metabolite identifiers between different databases (HMDB, PubChem and others)

BinBase

Software tool and database to process, store and compare GC-TOF MS metabolomic data (LECO formats only)

miniX

Software tool and database to define study design parameters                                                                                   
that enables managing metabolomic data files for different platforms

MZmine Lipid Parameters, database and instructions

Parameters for processing lipid data including a csv database for automated peak list generation and annotation presented at Metabolomics Society conference, Glasgow 2013

Links to External Downloads

NIH Metabolomics Data repository

Prof. Shankar Subramaniam at UC San Diego will develop a public data repository for all NIH-funded regional metabolomics resource cores. The Fiehn laboratory is partnering in this effort.

 

mzMine Software tool to process and compare LC-MS metabolomic data files

XCMS Software tool to process and compare LC-MS metabolomic data files

LipidMAPS Resources for analyzing lipid metabolism data

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