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 <[email protected]>: > > 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 > >> [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. > > -- 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
