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Welcome To BioDAS.org

http://biodas.org/ will eventually be migrated to a wiki format. In the meantime, please continue to use the original site. If you want to pitch in and help this migration, send a note to the BioDAS discussion list.

About DAS

The Distributed Annotation System (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that annotations should not be provided by single centralized databases, but instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients.

DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers.

DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities.

What can I do with DAS ?

A number of sites and applications is available that are using DAS.

• IGB: http://genoviz.sourceforge.net

• Gbrowse: http://www.gmod.org/gbrowse_installation

• Ensembl: http://www.ensembl.org/info/data/external_data/das/ensembl_das.html

• Spice: http://www.efamily.org.uk/software/dasclients/spice/

• Dasty: http://www.ebi.ac.uk/das-srv/uniprot/dasty/content?ID=:dis=BioSapiens

• Dasty2: http://www.ebi.ac.uk/~rafael/pre_dasty2/

• Jalview: http://www.jalview.org

• PeppeR: http://biocomp.cnb.uam.es/das/PeppeR/

The Protocol

Currently there are two versions of the DAS protocol

• DAS/1

The original version 1 specification, written by Lincoln Stein and Robin Dowell, is the basis for a number of clients and servers. More than 200 DAS/1 servers are currently running worldwide including WormBase, FlyBase, Ensembl, TIGR, and UCSC. For a listing of all available DAS sources please proceed to http://www.dasregistry.org

• DAS/2

In light of lessons learned during the DAS/1 implementation, a transition to a more flexible and powerful protocol called DAS/2 is underway. This transition will occur slowly and DAS software will continue to support DAS/1 for some years to come. The evolution from DAS/1 to DAS/2 is very much a community-driven process, informed by a variety of RFCs (Requests for Comment) received from the user communty.

DAS/2 development officially commenced in July 2004 when a 2-year NIH grant was funded. Participating in the DAS/2 grant are Affymetrix, Cold Spring Harbor Lab, the European Bioinformatics Institute/Sanger Center, and Dalke Scientific.

Mailing Lists

There are currently two separate mailing lists for public discussions about DAS, one for DAS/1 and one for DAS/2. See the BioDAS mailing list page for more info.

CVS access

Want to contribute to the Wiki? please see some beginners instructions at the WikiGetStarted page.