Difference between revisions of "DAS/2"

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(New page: <big>'''The DAS/2 Protocol'''</big> == About DAS/1 == The original version 1 specification, written by Lincoln Stein and Robin Dowell, is the basis for a number of clients and servers. ...)
 
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[[Category:Documentation]]
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<big>'''The DAS/2 Protocol'''</big>
 
<big>'''The DAS/2 Protocol'''</big>
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== About DAS/2 ==
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DAS/2 is intended to be a more flexible and powerful version of the original  [[DAS/1]] specification. It was built to address the needs of distributing massive genomic data sets derived from high density microarray applications and Next (and Next Next) Generation Sequencing.  Unlike DAS/1, DAS/2 does not require data exchange through text based XML but allows for data distribution using any text or binary format. The two versions are not natively compatible. The DAS/2 code base consists of:
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# DAS/2 Specification:
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#* [http://biodas.org/documents/das2/das2_protocol.html DAS/2.0 specification] (stable)
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#* [[DAS/2.1/Spec| DAS/2.1 specification]] (under development)
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# (Inactive ?) [http://das.biopackages.net/das/genome A publicly accessible DAS/2 server implementation] (open source code available from the [http://www.gmod.org/ GMOD project])
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# [http://genoviz.sourceforge.net The GenoViz open-source DAS/2 client implementation]
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# [http://sourceforge.net/projects/dasypus An open-source client library and server validation suite]
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See [[DAS/2#CVS Access]] for details on retrieving code related to these projects.
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=== DAS/2 History ===
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DAS/2 diverged from [[DAS/1]] as a result of a variety of [http://biodas.org/RFCs/index.html RFCs (Requests for Comment)] posted on the DAS mailing list from users and implementers of the DAS spec over the first several years after DAS was originally introduced. As of November 2006, the [http://biodas.org/documents/das2/das2_get.html retrieval portion of the DAS/2 spec] has stabilized. Implementers and service providers can rely on this for their DAS/2-based development efforts.
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Work on what became the DAS/2.0 specification "officially" began in July 2004 when funding was awarded for a 2-year NIH grant for DAS/2 development ([http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6712060&p_grant_num=1R01HG003040-01&p_query=(DAS)&ticket=15416031&p_audit_session_id=72191905&p_audit_score=100&p_audit_numfound=1&p_keywords=DAS abstract], [http://biodas.s3.amazonaws.com/das2grant/DAS2+Grant+Proposal+Feb2003.doc full proposal]). The grant was subsequently extended, and the grant funding period ended October 2007 ([http://biodas.s3.amazonaws.com/das2grant/DAS2+Grant+Final+Progress+Report+Aug2008.doc final progress report]). Participating in the DAS/2 grant were Affymetrix, Cold Spring Harbor Lab, the European Bioinformatics Institute/Sanger Center, and Dalke Scientific.
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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 [http://lists.open-bio.org/pipermail/das2/2008-October/001055.html DAS proxy server is in development] that will permit a DAS/1 server to be accessed by DAS/2 clients.
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== DAS/2 Clients ==
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The following software packages support the client-side DAS/2 API for interacting with DAS/2-compliant servers:
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* [http://genoviz.sourceforge.net IGB - Integrated Genome Browser] - a DAS/2 reference implementation
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[[File:Igb.jpg | 800px]]
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* [http://www.gmod.org/GBrowse GBrowse - Generic Genome Browser]
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* [http://cabio.nci.nih.gov/NCICB/infrastructure/cacore_overview/caBIO caBIO Infrastructure Objects] ''(confirm this)''
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== DAS/2 Servers ==
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The following software packages operate as servers capable of providing data in response to queries conforming with the DAS/2 protocol:
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* [http://netaffxdas.affymetrix.com/das2 Affymetrix Public DAS/2 server]
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* [http://bioserver.hci.utah.edu:8080/DAS2DB/ Huntsman Cancer Institute's DAS/2 server]
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* [http://bioserver.hci.utah.edu:8080/DAS2DB/genopub HCI's GenoPub DAS/2 GUI] ('''login''': guest, '''pw''': guest) - A Flex/MySQL web application for organizing, annotating, and authorizing genomic annotations for distribution using the GenoViz DAS/2 server
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[[File:Genopub.jpg | 800px]]
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* [http://das.biopackages.net/das/genome Biopackages DAS/2 server] - (inactive?) a DAS/2 reference implementation
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== DAS/2 Validation Suite ==
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See [[Das2Validation]].
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== About DAS/1 ==
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== Publishing, Discovering, and Registering DAS/2 sources ==
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Currently, the [http://www.dasregistry.org DasRegistry] does not support DAS/2 services.
  
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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 [http://www.wormbase.org/ WormBase], [http://www.flybase.org/ FlyBase], [http://www.ensembl.org/ Ensembl], [http://www.tigr.org/ TIGR], [http://genome.ucsc.edu/ UCSC], and [http://www.ebi.ac.uk/das-srv/uniprot/das UniProt]. A number of websites and software applications are based on DAS.
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As a temporary fix, download the 'das2Registry.xml' file from the [http://genoviz.svn.sourceforge.net/viewvc/genoviz/trunk/das2_server/resources/ GenoViz Project], add an entry, and email it back to [mailto:genoviz-devel@lists.sourceforge.net GenoViz] or [mailto:das@biodas.org BioDas]. If you have access to the GenoViz SVN, modify it directly.
  
  
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The DAS/1 specification is currently available in version 1.53 from
 
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http://www.biodas.org/documents/spec.html
 
  
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== Clients ==
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== Global Sequence Identifiers==
  
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a list of DAS/1 clients here
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See [[GlobalSeqIDs]]
  
  
  
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== How to set up a DAS/1 server ==
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== Feedback and Bug Reports ==
  
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In general it is quite easy to set up DAS server. All the server implementations are easy to set up.
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A general forum for advice on DAS/2-related issues is the [http://biodas.org/mailman/listinfo/das discussion list].
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Most server implementations allow easy setup using ready provided data-adaptors (e.g. for GFF files).
 
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For custom data simple plugins can be written to quickly provide your data via DAS.
 
  
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DAS server implementations are available in several programming languages:
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To submit or view bug reports in DAS/2-related software, use one of the links below, depending on the affected component.
  
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* Perl
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* DAS/2 Specification:
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[http://www.sanger.ac.uk/Software/analysis/proserver/ Proserver]
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**  http://bugzilla.open-bio.org/
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[http://biodas.org/servers/LDAS.html LDAS]
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* Reference Server (GMOD Project - select category 'DAS2'):
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**    http://sourceforge.net/tracker/?group_id=27707&atid=391291
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* Reference Client (IGB) - select category 'DAS':
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**    http://sourceforge.net/tracker/?group_id=129420&atid=714744
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* Validation Suite (Dasypus):
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**    https://sourceforge.net/tracker/?group_id=138271&atid=740641
  
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* Java
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== CVS Access ==
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[http://www.derkholm.net/thomas/dazzle/ Dazzle]
 
  
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== Publishing and Discovery of DAS/1 sources ==
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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.
  
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The DAS/1 specification does not define how to publish or discover DAS sources. Due to the
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* DAS/2 spec:
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success of DAS and the large number of sources that are spread around the world it is not easy
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** <code>:pserver:cvs@cvs.biodas.org:/home/repository/biodas</code>
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to keep track of these. The DAS registration server at [http://www.dasregistry.org www.dasregistry.org]
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*** (login password="cvs", directory=das/das2, XML schema for retrieval spec: das2_schemas.rnc)
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provides a repository where people can publish and  share their DAS sources with the community.
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* [http://genoviz.sourceforge.net DAS/2 Client reference implementation] ("IGB")
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* [http://gmod.org DAS/2 Server reference implementation] (see das2 package)
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* [http://sourceforge.net/projects/dasypus/ DAS/2 validation suite] ("Dasypus")
  
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The DAS registry provdies a Web interface so users can search for available DAS source. For
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See http://www.open-bio.org/wiki/SourceCode for general pointers about anonymous access to [http://open-bio.org open-bio.org]-hosted source code.
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DAS-clients an XML interface is available that allows to obtain the listing programmatically.
 
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For more info on this please see the [http://www.dasregistry.org/help_scripting.jsp documentation].
 

Latest revision as of 16:17, 16 November 2010


The DAS/2 Protocol

About DAS/2

DAS/2 is intended to be a more flexible and powerful version of the original DAS/1 specification. It was built to address the needs of distributing massive genomic data sets derived from high density microarray applications and Next (and Next Next) Generation Sequencing. Unlike DAS/1, DAS/2 does not require data exchange through text based XML but allows for data distribution using any text or binary format. The two versions are not natively compatible. The DAS/2 code base consists of:

  1. DAS/2 Specification:
  2. (Inactive ?) A publicly accessible DAS/2 server implementation (open source code available from the GMOD project)
  3. The GenoViz 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 diverged from DAS/1 as a result of a variety of RFCs (Requests for Comment) posted on the DAS mailing list from users and implementers of the DAS spec over the first several years after DAS was originally introduced. As of November 2006, the retrieval portion of the DAS/2 spec has stabilized. Implementers and service providers can rely on this for their DAS/2-based development efforts.

Work on what became the DAS/2.0 specification "officially" began in July 2004 when funding was awarded for a 2-year NIH grant for DAS/2 development (abstract, full proposal). The grant was subsequently extended, and the grant funding period ended October 2007 (final progress report). Participating in the DAS/2 grant were 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.

DAS/2 Clients

The following software packages support the client-side DAS/2 API for interacting with DAS/2-compliant servers:

Igb.jpg


DAS/2 Servers

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

Genopub.jpg


DAS/2 Validation Suite

See Das2Validation.


Publishing, Discovering, and Registering DAS/2 sources

Currently, the DasRegistry does not support DAS/2 services.

As a temporary fix, download the 'das2Registry.xml' file from the GenoViz Project, add an entry, and email it back to GenoViz or BioDas. If you have access to the GenoViz SVN, modify it directly.


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.

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.

See http://www.open-bio.org/wiki/SourceCode for general pointers about anonymous access to open-bio.org-hosted source code.

Retrieved from "http://biodas.open-bio.org/w/index.php?title=DAS/2&oldid=210"