SetupX and BinBase

Query BinBase for compounds

This is the main site to compare mass spectra by compound names, by BinBase identifiers or even by your GC/MS spectra that you have acquired on a different platform! The site also gives overview about positive detection of metabolites in the diverse set of species and organs analyzed at the UC Davis Genome Center (over 15,000 samples of more than 40 species)

[publication] Setup and Annotation of Metabolomic Experiments

Unbiased metabolomic surveys are used for physiological, clinical and genomic studies to infer genotype-phenotype relationships. Long term reusability of metabolomic data needs both correct metabolite annotations and consistent biological classifications. We have developed a system that combines mass spectrometric and biological metadata to achieve this goal. [...]

SetupX: Get started ...

To submit samples to the Lab the SetupX-System is used to capture the metadata about your experiment and samples. SetupX allows you to enter experimental designs for the metabolomics research lab at the UC Davis Genome Center.

[publication] A Public Study Design Database for Metabolomic Projects

Metabolomic databases are useless without accurate description of the biological study design and accompanying metadata reporting on the laboratory workflow from sample preparation to data processing. Here we report on the implementation of a database system that enables investigators to detail and set up a biological experiment, and that also steers laboratory workflows by direct access to the data acquisition instrument.[...]

[HowTo] BinBase - features, documentaion and FAQ

Documentation of the features, documentation and FAQ regarding BinBase

[HowTo] SetupX

Short descriptions on how to accomplish certain task on SetupX.

[publication] Current Progress in computational metabolomics

David S.Wishart wrote: "SetupX, developed by the Fiehn laboratory at UCD, is an excellent example of a web-based metabolomics LIMS. It is XML compatible and built around a relational database management core. It is particularly oriented towards the capture and display of GC–MS metabolomic data through its metabolic annotation database called BinBase."

SetupX the DeveloperBlog

The SetupX DeveloperBlog describes the changes made to the official release of SetupX. This includes new Features and Bug Fixes.

Download SetupX

Here you can find the sources of SetupX for download.

SetupX Poster Boston 2008

SetupX Poster shown at the Boston Metabolomics Conference 2008

BinBase Download

the BinBase database system download link

SetupX the DeveloperBlog started

The SetupX DeveloperBlog describes the changes made to the official release of SetupX. This includes new Features and Bug Fixes.