Difference between revisions of "DasFAQ"
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| + | == Which version of DAS should I be using? == | ||
| + | |||
| + | In short, "DAS" usually refers to the original version of the protocol. 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. Though the specification is now "frozen" and therefore considered stable, there exist few solid implementations. However, many of of the technical improvements in DAS/2 are now beginning to be adopted in DAS. | ||
== What applications are the actual "DAS clients"? == | == What applications are the actual "DAS clients"? == | ||
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== What DAS client should I use? == | == What DAS client should I use? == | ||
| − | Examples of DAS applications are listed on both the [[DAS/1#Clients]] and [[DAS/2#Clients]] pages. | + | Examples of DAS applications are listed on both the [[DAS/1#Clients|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 [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: | |
| − | |||
| − | around an existing DAS | ||
| − | clients to interact with existing DAS | ||
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 | ||
| − | DAS | + | 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. | ||
| + | |||
| + | == 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 [[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 | ||
Revision as of 17:22, 30 September 2009
DAS Frequently Asked Questions
Contents
- 1 Which version of DAS should I be using?
- 2 What applications are the actual "DAS clients"?
- 3 What DAS client should I use?
- 4 Are DAS and DAS/2 designed to interoperate? For example, will I be able to use a DAS/2 client and a DAS server?
- 5 I am totally confused, what should I do?
- 6 How does one retrieve genomic coordinates from a list of gene names or Entrez Gene IDs using DAS/2?
Which version of DAS should I be using?
In short, "DAS" usually refers to the original version of the protocol. 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. Though the specification is now "frozen" and therefore considered stable, there exist few solid implementations. However, many of of the technical improvements in DAS/2 are now beginning to be adopted in DAS.
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
