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