Hi Dan,
DAS clients tend to be different depending on the type of data you're
looking at, and have different capabilities. For example, Ensembl is a
well supported client for (mostly) genomic data, and implements all the
most recent developments such as the DAS registry (via the sources
command). However it makes no use of reference servers, instead all
reference data is stored locally in a database. Dasty is more focussed
on protein data. GBrowse is another genomic client, but IIRC does not
know about the DAS registry.
Regarding setting up a local DAS registry, what is this for? If for
instance you were using Ensembl, any server that implements the sources
command can potentially be a "registry" from a programmatic point of
view, so unless you want to have a manual process where you can use a
GUI to register a souce, you probably don't need to implement a copy of
the real thing.
Looks like the biodas wiki has been getting spammed, must have started
recently. I'll talk to the admins about sorting it out. We'll probably
need to update the registration process.
Cheers,
Andy
Dan Bolser wrote:
Hi all,
I'm relatively new to DAS, and I have been playing with setting up a
DAS server using Dazzle. Now that I have created my reference and
annotation data sources, naturally enough I would like to start
browsing and visualizing the data. So...
Q1) Which DAS client do you recommend for a beginner working with Dazzle?
I am working in a Linux OS, and I am looking at gene predictions on a
chromosome as well as 'similarity' features between the chromosome and
several 'clones' from a closely related organism.
To organize my research into the various clients available, I created
the following page on Wikipedia:
http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients
That table is still quite rough, so please feel free to contribute
information there. I put the table into a sub-page of the DAS page so
that sites like http://www.biodas.org/ can easily 'transclude' this
information. I'm not sure if that's sensible or not yet, so let me
know what you think.
Since we are exploring the various possibilities of using DAS with our
projects, is it possible to set up a local (private) DAS registry
server? This would be useful for testing purposes, especially as we
may be initially working with unpublished data.
Q2) What steps are required for setting up a local or a secure DAS registry?
Thanks very much for any help with the above two questions.
Dan
P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange
data encoding that I don't understand? I've seen more than one page
that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss -
Should I go ahead and delete this pages?
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