Difference between revisions of "DAS/2"

Revision as of 03:00, 27 February 2007

The DAS/2 Protocol

About DAS/2

DAS/2 is a more flexible and powerful version of the original DAS/1. The DAS/2 code base consists of:

1. The DAS/2 specification
2. A publically accessible DAS/2 server implementation (open source code available from the GMOD project)
3. An open-source DAS/2 client implementation
4. An open-source client library and server validation suite

See DAS/2#CVS Access for details on retrieving code related to these projects.

DAS/2 History

DAS/2 evolved from DAS/1 through a community-driven process, informed by a variety of RFCs (Requests for Comment) received from the community of users and implementers of the spec. As of November 2006, the retrieval portion of the DAS/2 spec has stabilized. Implementers can rely on this for their DAS/2-based development efforts.

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.

Given that the DAS/2 specification is not backward compatible with the DAS/1 version, existing DAS software will continue to support DAS/1. A DAS proxy server is in development that will permit a DAS/1 server to be accessed by DAS/2 clients.

Clients

The following software packages operate as clients capable of interacting with servers supporting the DAS/2 protocol:

• IGB - Integrated Genome Browser
• GBrowse - Generic Genome Browser

Servers

The following software packages operate as servers capable of providing data in response to queries conforming with the DAS/2 protocol:

• Biopackages DAS/2 server - a DAS/2 reference implementation
• Affymetrix Public DAS/2 server

Validation Suite

See Das2Validation.

Publishing and Discovery of DAS/2 sources

See DasRegistry

Global Sequence Identifiers

See GlobalSeqIDs

Feedback and Bug Reports

A general forum for advice on DAS/2-related issues is the discussion list.

To submit or view bug reports in DAS/2-related software, use one of the links below, depending on the affected component.

• DAS/2 Specification:
  • http://bugzilla.open-bio.org/
• Reference Server (GMOD Project - select category 'DAS2'):
  • http://sourceforge.net/tracker/?group_id=27707&atid=391291
• Reference Client (IGB):
  • http://sourceforge.net/tracker/?group_id=129420&atid=714744
• Validation Suite (Dasypus):
  • https://sourceforge.net/tracker/?group_id=138271&atid=740641

CVS Access

There are separate repositories for the DAS/2 specification, DAS/2 client and server reference implementations, and the validation suite. These are for developers only since they do not represent stable releases and may contain modifications that contain bugs. The one exception is the schema for the retrieval portion of the DAS/2 spec, which is now stable.

• DAS/2 spec:
  • :pserver:cvs@cvs.biodas.org:/home/repository/biodas
    • (login password="cvs", directory=das/das2, XML schema for retrieval spec: das2_schemas.rnc)
• DAS/2 Client reference implementation ("IGB")
• DAS/2 Server reference implementation (see das2 package)
• DAS/2 validation suite ("Dasypus")