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 <[email protected]>: > > 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 > >> [email protected] > >> http://lists.open-bio.org/mailman/listinfo/das > >> From - Mon > > > _______________________________________________ > DAS mailing list > [email protected] > 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. _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
