MetWare - Applications, Databases and Workflows for Metabolomics
The MetWare project is a collaboration between - but not limited to - several metabolomics groups in the Netherlands and Germany
Our goal is to develop distributed databases and analysis tools for metabolomics research. They will cover
- a Repository for raw data
- associated experiment metadata, covering at least MIAMET and ArMet
- preprocessed data (individual peaks or (tandem-MS) spectra or MSn trees)
- a Metabolite library with reference data
- annotation and identification joining reference and preprocessed data
The architecture is based on several other (mostly open source) projects and standards:
- The databases will be accessible through either BioMoby web services or the BioMart framework
- Frontends will be based on command line tools, the Taverna workflow engine or the Bioclipse framework
- Mass Spectrometry processing will be based on XCMS from BioConductor
MetWare is organized in a number of interdepending subprojects (the source code is in SVN).
- MetWeb: the HTML GUI to the data warehouse
- ProtoRAW: the prototype storage facility
- BigMet: module that contains the MetWare ontology and SQL design
- MetBeans: Java Beans library to interact with SQL database. Building on top of this is the importer for the [ISATab] format.
- MetFlow: a collection of (Taverna) Workflows around typical metabolomics tasks
- MetFrag: consists of a java library, a Web GUI and BioMoby Services to search molecular databases (such as [KEGG] or [PubChem] using tandem-MS spectra.
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mzAnnotate is a XML based data exchange format for annotated mass spectra.The discussions on mzAnnotate take place at the [mailing list] of the [data exchange group] of the [Metabolomics Society], the results will be collected in this wiki.
The best way to get in touch with the MetWare community is via the mailing lists.
Internet Relay Chat
An alternative to mailing lists is the #metware channel on irc.freenode.net. However note that this is probably only useful for quick and small questions and larger discussions are best handled on the mailing lists. The IRC channel is also used to coordinate hack sessions from time to time.