Difference between revisions of "DasFAQ"

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[[Category:Documentation]]
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<big>'''DAS Frequently Asked Questions'''</big>
 
<big>'''DAS Frequently Asked Questions'''</big>
  
 
__TOC__
 
__TOC__
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== Should I be using DAS or DAS/2? ==
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"DAS" usually refers to version 1 of the protocol, sometimes called DAS/1. It continues to evolve and be supported, and is the basis of implementations for the vast majority of clients and servers. "DAS/2" is a separate protocol that is inspired by many of the same principles as DAS, but is not backwards compatible. One of the key differences is that DAS/2 allows annotations to be returned using any text or binary data format enabling the distribution of massive microarray and Next Generation Sequencing data sets.  DAS/1 requires data distribution through text based DAS XML.
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== Which version of DAS/1 should I use? ==
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As of 19th October 2010, the latest official version of DAS/1 is [[DAS1.6|version 1.6]]. Compatibility with previous versions is covered on the [[DAS 1.6 Migration]] page.
  
 
== What applications are the actual "DAS clients"? ==
 
== What applications are the actual "DAS clients"? ==
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DAS applications generally take the form of graphical genome browsers,
 
DAS applications generally take the form of graphical genome browsers,
 
protein feature/structure browsers, and even gene information browsers.
 
protein feature/structure browsers, and even gene information browsers.
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Examples of DAS applications are listed on both the [[DAS/1#Clients]] and [[DAS/2#Clients]] pages.
 
  
 
For an example of how Ensembl acts as a DAS client for gene information
 
For an example of how Ensembl acts as a DAS client for gene information
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http://www.ebi.ac.uk/~rafael/das/index.php?display=clients
 
http://www.ebi.ac.uk/~rafael/das/index.php?display=clients
  
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== Are DAS/1 and DAS/2 designed to interoperate? For example, will I be able to use a DAS/2 client and a DAS/1 server? ==
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See also: [[#What DAS client should I use?]]
  
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DAS/2 is a complete redesign of the original DAS/1 specification, so direct interoperation is not
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== What DAS client should I use? ==
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possible. However, the [http://biodas.org/documents/das2/das2_protocol.html DAS/2 spec] has all of the capabilities of the [http://www.biodas.org/documents/spec.html DAS/1 spec] (and more!).
 
  
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As proof of this, a proxy adapter is being developed that will provide a DAS/2 interface  
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Examples of DAS applications are listed on both the [[DAS/1#Clients|DAS Clients]] and [[DAS/2#Clients]] pages.
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around an existing DAS/1 server, allowing DAS/2
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clients to interact with existing DAS/1 servers:
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== Are DAS and DAS/2 designed to interoperate? For example, will I be able to use a DAS/2 client and a DAS server? ==
 +
 
 +
DAS/2 is a complete redesign of the original DAS specification, so direct interoperation is not
 +
possible. However, the [http://biodas.org/documents/das2/das2_protocol.html DAS/2 spec] has all of the capabilities of the [http://www.biodas.org/documents/spec.html DAS spec] (and more!).
 +
 
 +
A proxy adapter is being developed that will provide a DAS/2 interface  
 +
around an existing DAS server, allowing DAS/2
 +
clients to interact with existing DAS servers:
 
http://lists.open-bio.org/pipermail/das2/2006-October/000867.html
 
http://lists.open-bio.org/pipermail/das2/2006-October/000867.html
  
 
To fully realize 1 <-> 2 interoperation, there would need to be a
 
To fully realize 1 <-> 2 interoperation, there would need to be a
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DAS/1 proxy adapter for DAS/2 servers, to permit DAS/1 clients to interact
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DAS proxy adapter for DAS/2 servers, to permit DAS clients to interact
 
with DAS/2 servers. Whether such a utility will be needed or developed remains to be seen.
 
with DAS/2 servers. Whether such a utility will be needed or developed remains to be seen.
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== I am totally confused, what should I do? ==
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 +
Unfortunately due to the wide application and abstract nature of DAS, it can be difficult to find information at the right level for each person's individual perspective. It is highly recommended to ask questions on one of the mailing lists, see the [[BioDAS:Community_Portal|Community Portal]] for details.
  
 
== How does one retrieve genomic coordinates from a list of gene names or Entrez Gene IDs using DAS/2? ==
 
== How does one retrieve genomic coordinates from a list of gene names or Entrez Gene IDs using DAS/2? ==
  
 
See this thread on the DAS/2 discussion list: http://lists.open-bio.org/pipermail/das2/2007-January/000967.html
 
See this thread on the DAS/2 discussion list: http://lists.open-bio.org/pipermail/das2/2007-January/000967.html

Latest revision as of 13:11, 19 October 2010


DAS Frequently Asked Questions

Should I be using DAS or DAS/2?

"DAS" usually refers to version 1 of the protocol, sometimes called DAS/1. It continues to evolve and be supported, and is the basis of implementations for the vast majority of clients and servers. "DAS/2" is a separate protocol that is inspired by many of the same principles as DAS, but is not backwards compatible. One of the key differences is that DAS/2 allows annotations to be returned using any text or binary data format enabling the distribution of massive microarray and Next Generation Sequencing data sets. DAS/1 requires data distribution through text based DAS XML.

Which version of DAS/1 should I use?

As of 19th October 2010, the latest official version of DAS/1 is version 1.6. Compatibility with previous versions is covered on the DAS 1.6 Migration page.

What applications are the actual "DAS clients"?

DAS applications generally take the form of graphical genome browsers, protein feature/structure browsers, and even gene information browsers.

For an example of how Ensembl acts as a DAS client for gene information browsing, see the "Gene DAS Report" section of this page: http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000165029

Here's an interesting review of EBI DAS clients: http://www.ebi.ac.uk/~rafael/das/index.php?display=clients

See also: #What DAS client should I use?

What DAS client should I use?

Examples of DAS applications are listed on both the DAS Clients and DAS/2#Clients pages.

Are DAS and DAS/2 designed to interoperate? For example, will I be able to use a DAS/2 client and a DAS server?

DAS/2 is a complete redesign of the original DAS specification, so direct interoperation is not possible. However, the DAS/2 spec has all of the capabilities of the DAS spec (and more!).

A proxy adapter is being developed that will provide a DAS/2 interface around an existing DAS server, allowing DAS/2 clients to interact with existing DAS servers: http://lists.open-bio.org/pipermail/das2/2006-October/000867.html

To fully realize 1 <-> 2 interoperation, there would need to be a DAS proxy adapter for DAS/2 servers, to permit DAS clients to interact with DAS/2 servers. Whether such a utility will be needed or developed remains to be seen.

I am totally confused, what should I do?

Unfortunately due to the wide application and abstract nature of DAS, it can be difficult to find information at the right level for each person's individual perspective. It is highly recommended to ask questions on one of the mailing lists, see the Community Portal for details.

How does one retrieve genomic coordinates from a list of gene names or Entrez Gene IDs using DAS/2?

See this thread on the DAS/2 discussion list: http://lists.open-bio.org/pipermail/das2/2007-January/000967.html

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