[DAS] Question about DAS clients and DAS registry servers

[Jonathan Warren]

Ok if your sources are in-house then I'd use GBrowse as it's easier to
set up and you can point it at both a das reference server and
annotation server (which I don't think you can do with ensembl). GBrowse
can also be set up to be a DAS source itself just by setting the
mapmaster in the configuration file. Note: GBrowse is perl based and the
registry is Java (servlets and JSP) based. Also note that most of the
clients you list on the table use DAS 1.* whereas IGB uses DAS2. There
are far more das sources available for DAS1 than 2 but some efforts are
being made at allowing them to communicate with each other.




On Mon, 2009-01-12 at 13:21 +0000, Dan Bolser wrote:
> Hi Jonathan,
> 
> Thanks very much for your reply. My comments are inline below:
> 
> 
> 2009/1/12 Jonathan Warren <jw12 at sanger.ac.uk>:
> > Hi Dan
> >
> > Thanks for putting up the table - I'll add some info to it shortly.
> 
> Cheers, that would be great!
> 
> 
> > The dasregistry source code is downloadable using subversion at
> > http://www.derkholm.net/svn/repos/dasregistry/trunk/
> >
> > You will also need a mysql instance set up. I can send you some info on
> > that if you wish.
> 
> Please provide as much information as possible! :-D
> 
> 
> > There are many dependencies and configurations needed- so it may take a
> > while to set up a fully fledged version - it may be better to experiment
> > with your sources using the real one - I'll help you out if you need
> > clarification on anything such as error messages and logs. Or is it that
> > you don't want to release your data to the world and only want an in
> > house version?
> 
> Yes. In the long run we will be making all our data publicly
> available, however, for R&D purposes and leading up to publication of
> the source data we would like to experiment with an in-house registry.
> Also, I think it would be a convenient administrative / organizational
> tool for us. i.e. to keep track of the various data sources
> (experimental or otherwise) that are being developed in-house.
> 
> 
> > I think I would recomment using ensembl to connect to your sources in
> > the first instance - but if you want the client to sit on your
> > desktop/local server then maybe GBrowse (this is for genomic annotations
> > obvioyusly)?
> 
> Sorry for my ignorance, but can I ask if you mean that I should use
> ensembl remotely (on some server 'out there') and point it at my local
> reference / annotation server? The problem is again that both are
> internal, with no outfacing interface. In any case, its clear that I
> need to read more about ensembl, so feel free to ignore this question.
> 
> 
> In another email you said: "You can just put the table onto biodas.org
> if you wish..."
> 
> I see this point. I am never sure how 'external' wikis should interact
> with Wikipedia when overlapping data is available in both. In this
> case I thought I'd edit WP, but please feel free to move the table to
> somewhere within biodas.org - I wasn't immediately sure where to put
> it, which is partly why I picked WP.
> 
> 
> Thanks very much for the information above,
> 
> Dan.
> 
> > On Mon, 2009-01-12 at 12:11 +0000, 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?
> >> _______________________________________________
> >> DAS mailing list
> >> DAS at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/das
> >
> >
> >
> > --
> >  The Wellcome Trust Sanger Institute is operated by Genome Research
> >  Limited, a charity registered in England with number 1021457 and a
> >  company registered in England with number 2742969, whose registered
> >  office is 215 Euston Road, London, NW1 2BE.
> >



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.