[DAS] Question about DAS clients and DAS registry servers

[Jonathan Warren]

Dan - have you any timescales in mind for setting up an internal
registry? I am looking at the DAS documentation available at the moment
and could write a DASRegistry doc.

Are you happy with using eclipse, jsp and servlets in tomcat or resin
containers?

On Mon, 2009-01-12 at 13:34 +0000, Dan Bolser wrote:
> 2009/1/12 Andy Jenkinson <andy.jenkinson at ebi.ac.uk>:
> > 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.
> 
> I see what you mean, but what I'm calling 'in-house' could potentially
> comprise several different servers at several different locations. The
> theory is that they would all be part of a private 'consortium', which
> would ultimately become part of the DAS registry proper. In so far as
> we would like to keep track of the different DAS servers that we have
> 'in-house', I thought a registry could be a good solution.
> 
> 
> > 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.
> 
> On several wikis using a 'captcha', I found that the following set
> rules strikes the right balance between keeping spam down and allowing
> unrestrictive access to users:
> 
> 0) Any user can edit the wiki, because registration puts people off.
> 1) On any edit, present any anonymous user with a captcha.
> 2) Registration requires a captcha.
> 3) Never present a registered user with a captcha.
> 
> In the MediaWiki config that looks like this:
> 
> // Fix the default captcha behaviour
> $wgGroupPermissions['*'            ]['skipcaptcha'] = false;
> $wgGroupPermissions['user'         ]['skipcaptcha'] = true;
> $wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true;
> $wgGroupPermissions['bot'          ]['skipcaptcha'] = true; // registered bots
> $wgGroupPermissions['sysop'        ]['skipcaptcha'] = true;
> 
> $wgCaptchaTriggers['edit']          = true;
> $wgCaptchaTriggers['create']        = true;
> $wgCaptchaTriggers['createaccount'] = true;
> 
> (all other permissions having their default values)
> 
> 
> Thanks for the info above,
> Dan.
> 
> > 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?
> >> _______________________________________________
> >> DAS mailing list
> >> DAS at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/das
> >> From - Mon
> >
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