Main Page
From metware
Contents |
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.
To get started with development, check the Development Setup. You can almost always find some developers Some of our plans are outlined in the minutes of the DeveloperMeeting08.
YourKit is kindly supporting open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of innovative and intelligent tools for profiling Java and .NET applications. Take a look at YourKit's leading software products: [YourKit Java Profiler] and [YourKit .NET Profiler].
mzAnnotate
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.
Contact
The best way to get in touch with the MetWare community is via the mailing lists.
For queries regarding the design and development subscribe to metware-devel (Archives).
The active discussion on mzAnnotate takes place on the [data exchange mailing list] of the [Exchange format working group].
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.
