Links and Resources

 

 

 

 Rothamsted Research is one if eight institutes sponsored by the biotechnology and biological sciences research council

 

 

 

 

 

 

 

 

 

 

 

 

Instrumentation Links

 

Bruker Biospin NMR Manufacturer

Waters Corporation HPLC / MS Manufacturer

ThermoFinnigan MS Manufacturer

Agilent Agilent (ex Hewlett Packard) manufacture GC / GC-MS/ HPLC etc 

 

Pathways etc

 

KEGG The Kyoto encyclopedia of genes and genomes. Draws maps of metabolic pathways including active links to sequence data on the proteins that catalyse the steps, and the genes that encode them.

 

Biochemical pathways ExPASy Molecular Biology Server. The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE

 

Ligand LIGAND is a composite database consisting of: COMPOUND (a collection of chemical compounds that are related to various cellular processes) REACTION (a collection of reactions, mostly enzymatic reactions, involving those compounds) ENZYME (Enzyme Nomenclature by IUBMB and IUPAC)

 

123genomics 123Genomics, a Genomics, Proteomics and Bioinformatics Knowledge Base

 

Computer Simulation of Metabolism  This site describes some simple computer routines that can be used to interpret stable isotope and radioisotope tracer kinetics in terms of metabolic fluxes and compartmentation of pools.

 

EMP project queries for pathways, metabolic outlines, software, nomenclature (enzymes) etc.

Boehringer Mannheim "Biochemical Pathways" This page gives access to the digitized version of the Boehringer Mannheim "Biochemical Pathways" wall chart. Please note that the German publishing company Spektrum Akademischer Verlag Gmbh, Slevogtstrasse 3-5, 69126 Heidelberg owns the rights for commercial applications of the Biochemical Pathways. If you wish to use any of the information obtained from this site commercially please contact Ms. Ina Schibel at Spektrum Verlag for approval.

GEPASI Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any funtion of the model, perform metabolic control analysis and linear stability analysis.

 

PathDB PathDB™ is a functional prototype research tool for biochemistry and functional genomics. One of the key underlying philosophies of our project is to capture discrete metabolic steps. This allows us to build tools to construct metabolic networks de novo from a set of defined steps.

 

Biocyc is a collection of pathway/genome databases, all based on the Pathway Tools System developed at SRI. Two of these databases, Ecocyc for E. coli and Metacyc (pathways and enzymes from 150 species) are literature derived pathway/genome databases. Other Biocyc databases are computationally derived.

 

Aracyc is a literature derived pathway/genome database, curated by TAIR for Arabidopsis. This system is also based on the Pathway Tools system.

 

WIT WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models.

 

 

 

Metabolomics Companies

 

Metanomics

Phenomenome Discoveries

LemnaTech

Cogenics (previously Paradigm Genetics)

Large Scale Biology Corp.

 


 

 

Metabolomics Research Groups

 

Max Planck Institute of Molecular Plant Physiology Department of Molecular Physiology Metabolomic Analysis. Oliver Fiehn Group

 

The Sumner Group Analytical Chemistry and Mass Spectrometry at the Samuel Roberts Noble Foundation

 

Norwich Research Park metabolomics  This website is a forum for Norwich Research Park based researchers with an interest in Metabolomics

 

Cell cybernetics PRI Metabolomics group of Plant Research International, business unit headed by Raoul Bino

 

Iowa State U

 

Leibniz Inst. of Plant Biochem, Germany

 

Wageningen U, Netherlands

 

Imperial College, London

 

Michigan State U

 

Center for Novel Ag Products (CNAP), U of York 

 

Metabolomics at the John Innes Centre

 

Software / Database Links

 Umetrics Software company producing SIMCA-P for multivariate analysis

Infometrix Infometrix is a leading developer of software products in the field of chemometrics employing pattern recognition and modeling techniques for the analysis of multivariate data sets in chemistry and biotechnology. Products include Line-up and Pirouette

Advanced Chemistry Development (ACD) Spectroscopy / Databasing Software

spectroscopynow.com Online Spectroscopy Resource from Wiley

NIST A huge database of spectra and chemicals. (175,000 GC mass spectra of over 147,000 compounds), and AMDIS deconvolution software for GC-MS

 

ThermoGalactic Spectra library A free searchable database containing over 6,000 FTIR, Raman, MS, 13C & 1H NMR, UV/VIS, NIR and XRD spectra. Pure compounds include chemical formula, CAS number, chemical name, chemical structure and other chemical properties where available.

 

WILEY Wiley AccessPak 7th Edition (444,000 GC mass spectra of over 360,000 compounds)

 

SDBS Six different types of spectral database (including 21,800 GC mass spectra and over 25,000 NMR spectra)

 

SUGABASE SUGABASE is a carbohydrate-NMR database that combines CarbBank Complex Carbohydrate Structure Data (CCSD) with proton and carbon chemical shift values.

 

NMR Database of Lignin and Cell Wall Model Compounds This NMR database has been designed to aid plant cell wall chemists in general and lignin chemists in particular. By NMR Database compiling data from a series of model compounds run under strict acquisition conditions in three solvents.

 

Eigenvector Research, Inc.  A Chemometrics Research and Applications Company located in WA, USA.  

 

Pattern Recognition Systems AS A Norwegian company specializing in Multivariate Data Analysis.  

 

Statistical Solutions

Statistical Solutions has built an international reputation as a prominent provider of advanced leading-edge statistical software solutions.

 

The Mathworks

Matlab homepage

 

The Madison Metabolomics Consortium Database (MMCD)

A resource for mass spectromic (MS) and NMR based metabolomics research providing comprehensive information about small molecules of biological importance and support for high-throughput tools for identifying and quantifying compounds in biological fluids or cell extracts.