[DAS2] current status of DAS

[Rowan Kuiper]

I have a few questions. I’m a bioinformatics student and for an internship 
at the Erasmus University in Holland I have to investigate the current 
status of DAS. I’ve been trying to work with DAS a couple of weeks now and 
the impression I get is that it is a bit messy. Perhaps this is because I 
don’t understand DAS very well and can you explain it to me.

- First of all, will DAS2 ever be finished. I saw on  the biodas site that 
the 2 year  development started in 2004. But when I looked at sites that 
should propagate the development, DAS seems to be out of focus. You think 
DAS is still alive or is there something else that took its place?

- Why don’t all servers support all commands. Some reference servers for 
example don’t support the entry_point command. How do I request features 
when I don’t know which segments the server contains? I imagine that these 
great differences in how to use different servers could be very problematic 
when implementing a viewer.

- It seems that the only way to retrieve information from a server is to do 
a request for a certain region. Is there a way to ask for a specific 
features.

- Is the Sanger Registry Server reliable or is it something of the past? It 
would be very nice if all available sources where listed there but just a 
small part of the sources I found where in the list.

- When I have to serve data that needs some extension on the XML structure, 
would it be a problem to just do it. How would clients handle these 
extensions. Ignore them or somehow parse them?

- And last, one of the goals of DAS is to be able to integrate biological 
data. When I for example want to compare my data to EnsEMBL features I will 
have to set up my own server that serves features referenced to the same 
genome as the EnsEMBL features. So I wonder if there exists reference 
servers that contain the current genomes  of EnsEMBL, NCBI or UCSC.  I found 
http://das.ensembl.org/das/ensembl_Homo_sapiens_core_38_36 which always 
replies an out of memory error even with the entry_points command and 
http://das.ensembl.org/das/ensembl1834 which seems to work properly but its 
transcript server ens1834trans also returns out of memory errors.


I think that there are some people here that can tell me their view on the 
subject.
Thanks in advance,
Rowan Kuiper