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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== About DAS/1 ==
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== About DAS/2 ==
  
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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DAS/2 is a more flexible and powerful version of the original [[DAS/1]]. The DAS/2 code base consists of:
  
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# [http://biodas.org/documents/das2/das2_protocol.html The DAS/2 specification]
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# [http://das.biopackages.net/das/genome A publically 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 An open-source DAS/2 client implementation]
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# [http://sourceforge.net/projects/dasypus An open-source client library and server validation suite]
  
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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== DAS/2 History ==
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DAS/2 evolved from the DAS/1 version through a community-driven process, informed by a variety of [http://biodas.org/RFCs/index.html RFCs (Requests for Comment) received from the user community]. DAS/2 development officially commenced in July 2004 when a 2-year [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 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.
  
 
== Clients ==
 
== Clients ==
  
a list of DAS/1 clients here
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a list of DAS/2 clients here
 
 
  
  
== How to set up a DAS/1 server ==
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== How to set up a DAS/2 server ==
  
In general it is quite easy to set up DAS server. All the server implementations are easy to set up.
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server setup docs here
Most server implementations allow easy setup using ready provided data-adaptors (e.g. for GFF files).
 
For custom data simple plugins can be written to quickly provide your data via DAS.
 
  
DAS server implementations are available in several programming languages:
 
  
* Perl
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== Publishing and Discovery of DAS/2 sources ==
[http://www.sanger.ac.uk/Software/analysis/proserver/ Proserver]
 
[http://biodas.org/servers/LDAS.html LDAS]
 
  
* Java
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See [[DAS_registry]]
[http://www.derkholm.net/thomas/dazzle/ Dazzle]
 
  
== Publishing and Discovery of DAS/1 sources ==
 
  
The DAS/1 specification does not define how to publish or discover DAS sources. Due to the
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== Global Sequence Identifiers==
success of DAS and the large number of sources that are spread around the world it is not easy
 
to keep track of these. The DAS registration server at [http://www.dasregistry.org www.dasregistry.org]
 
provides a repository where people can publish and  share their DAS sources with the community.
 
  
The DAS registry provdies a Web interface so users can search for available DAS source. For
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See [[GlobalSeqIDs]
DAS-clients an XML interface is available that allows to obtain the listing programmatically.
 
For more info on this please see the [http://www.dasregistry.org/help_scripting.jsp documentation].
 

Revision as of 14:39, 21 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


DAS/2 History

DAS/2 evolved from the DAS/1 version through a community-driven process, informed by a variety of RFCs (Requests for Comment) received from the user community. 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.

Clients

a list of DAS/2 clients here


How to set up a DAS/2 server

server setup docs here


Publishing and Discovery of DAS/2 sources

See DAS_registry


Global Sequence Identifiers

See [[GlobalSeqIDs]