Tools and software

This is an unsorted collection of tools and software developed or in use by the EU-SOL project. These are all also available in the more specific folders.

JABBA

An aggregator for data on arabidopsis genes: search by AGI locus code and retrieve literature, images, functional classification and clones from many distributed databases using BioMoby web services.

AFAWE - protein function prediction

Automatic function prediction in a web services environment, an integrated user interface to sequence similarity searches, Interpro domain predictions and GO term assignments using the SIFTER phylogenomic tool. Includes a curation interface for manual annotation.

BioMoby dashboard

Explore the biomoby central registries: List services, data types and namespaces, register services etc., and call web services through a simple client. The dashboard is part of the BioMoby distribution available from http://biomoby.org and is made available here as Java web start. Dashboard requires full privileges as it writes a cache of Moby central data to your hard drive. We have signed it ourselves; if you are worried by this, download the BioMoby distribution and build Dashboard yourself.

SOLector: Aggregator for tomato genes

SOLector is a Mashup application using aggregators to retrieve and integrate information about a specific tomato gene/protein. Aggregators in general are software applications collecting syndicated web content to gather this for a simple viewing. SOLector uses Biomoby to automatically discover relevant data sources from the Biomoby registry, and automatically includes them in the search. SOLector is a Java application set up for web start.

Marker2sequence

Obtain the list of genes in a genetic region of interest, e.g. a QTL, defined by flanking markers.